This paper presents a characterization of the complete genome sequences of two novel viruses isolated using Streptomyces griseus. Destructrice is a podovirid bacteriophage with a 45,548-bp genome assigned to the actinobacteriophage cluster BF. Rikishi, assigned to cluster BE2, is a siphovirid bacteriophage with a 132,567-bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/f5233118cd0050ffc02bcc1b71ecb1dc.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Destructrice produces medium-sized, clear plaques, while Rikishi produces smaller, clear plaques. Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus bacteriophages Destructrice and Rikishi
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as a biocontrol agent in the food-processing industry, agriculture, and aquaculture (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two phages that infect Streptomyces griseus: Destructrice and Rikishi.\nDestructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in liquid media supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar and incubated for 2 days at 30°C. Two rounds of purification were performed by picking plaques and plating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques ranging 1-2.5 mm in diameter and Rikishi plaques measuring 1 mm (Figure 1). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a short tail and Rikishi a siphovirus morphology with a long tail (Figure 1, Table 1).\nPhage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020). \nGenomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator, using Actino_draft database v578, HHPred, using the PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software.\nDestructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (44859-46511 bp), no identifiable tape measure protein (podovirus), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a long genome (126524-133969 bp), tape measure protein, and terminal repeat (12484 bp). Rikishi has a DNA primase that is split into two reading frames, like other phages in clusters BE2, A, and BD (Cresawn et al., 2011; Russell and Hatfull, 2017). No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.\n\nData Availability\nDestructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029. \n\nTABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.\n\nPhage\tDestructrice\tRikishi\nLocation found\tLouisville, Kentucky\tAlbion, Illinois \nLocation coordinates\t38.20882 N, 85.75387 W \t38.43662 N, 88.07433 W\nCapsid diameter [nm ± SD (n)]\t63 ± 3 nm (n=5)\t85 ± 12 nm (n=5)\nTail length [nm ± SD (n)]\t16 ± 2 nm (n=5)\t364 ± 30 nm (n=5)\nGenome size (bp)\t45548\t132567\nApproximate coverage (x)\t4540\t1582\nNumber of reads\t2.9 M\t1.9 M\nGC content (%)\t59.80%\t49.40%\nDirect terminal repeat length\t265\t12484\nCluster\tBF\tBE2\nNumber of protein coding genes\t63\t245\nNumber of tRNAs\t21 tRNAs\t42 tRNAs and 1 tmRNA\nGenBank accession no.\tPX234433\tPV876926\nSRA accession no.\tSRX28484007\tSRX28484029\nIsolated by\tK. Tyler and P. Kocher\tD. Seiler and D. Wolfe\nAltschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[],"curatorReviews":[]},{"id":"a3a90951-33cc-43a4-bb71-674dcd89cafd","decision":"revise","abstract":"This paper presents a characterization of the complete genome sequences of two novel viruses isolated using Streptomyces griseus. Destructrice is a podovirid bacteriophage with a 45,548-bp genome assigned to the actinobacteriophage cluster BF. Rikishi, assigned to cluster BE2, is a siphovirid bacteriophage with a 132,567-bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/f5233118cd0050ffc02bcc1b71ecb1dc.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Destructrice produces medium-sized, clear plaques, while Rikishi produces smaller, clear plaques. Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus bacteriophages Destructrice and Rikishi
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as a biocontrol agent in the food-processing industry, agriculture, and aquaculture (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two phages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in liquid media supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar and incubated for 2 days at 30°C. Two rounds of purification were performed by picking plaques and plating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques ranging 1-2.5 mm in diameter and Rikishi plaques measuring 1 mm (Figure 1). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a short tail and Rikishi a siphovirus morphology with a long tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator, using Actino_draft database v578, HHPred, using the PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software.
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (44859-46511 bp), no identifiable tape measure protein (podovirus), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a long genome (126524-133969 bp), tape measure protein, and terminal repeat (12484 bp). Rikishi has a DNA primase that is split into two reading frames, like other phages in clusters BE2, A, and BD (Cresawn et al., 2011; Russell and Hatfull, 2017). No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Phage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | PV876926 |
SRA accession no. | SRX28484007 | SRX28484029 |
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[{"reviewer":{"displayName":"Maria Diane Gainey Dr."},"openAcknowledgement":true,"status":{"submitted":true}},{"reviewer":{"displayName":"Adam D Rudner"},"openAcknowledgement":null,"status":{"submitted":false}},{"reviewer":{"displayName":"Dustin Edwards"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"3e44521a-8b67-4b2a-bbdc-21fefd42f1bd","decision":"revise","abstract":"This paper describes the complete genome sequences of two novel bacteriophages isolated using Streptomyces griseus. Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A.","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/ce141fcb272a85c0445e25ee4917ff4b.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Destructrice produces medium-sized, clear plaques (1.70 ± 0.397 mm), while Rikishi produces smaller, clear plaques (0.83 ± 0.322 mm). Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus phages Destructrice and Rikishi virion and plaque morphology
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as biocontrol agents in the food-processing, agriculture, and aquaculture industries (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two bacteriophages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in nutrient broth (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose, and was incubated for 2 days at 30°C. Two rounds of purification were performed by picking individual plaques and replateing, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques 1.70 ± 0.997 mm in diameter (n= 86) and Rikishi plaques 0.83 ± 0.322 mm (n=27) (Figure 1). Plaques were measured using the ViralPlaque macro on Fiji (Cacciabue et al., 2019). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a very short (16 ± 2 nm) tail and Rikishi a siphovirus morphology with a long (364 ± 30 nm) tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator (Actino_draft database v578), HHPred (PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases) (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (cluster range = 44859-46511 bp), no identifiable tape measure protein (absent in annotated podovirus phage), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a long genome (cluster range = 126524-133969 bp), a long tape measure protein (6300 bp), and a long terminal repeat (12484 bp). Rikishi has a DNA primase that is split into two reading frames, like other phages in clusters BE2, A, and BD (Cresawn et al., 2011; Russell and Hatfull, 2017). No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Bacteriophage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | |
SRA accession no. | ||
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cacciabue M, Currá A, Gismondi MI. 2019. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7: e7729.
","pubmedId":"","doi":"10.7717/peerj.7729"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[],"curatorReviews":[]},{"id":"cee5c9e9-dfee-47e3-a129-9354e5b06281","decision":"revise","abstract":"This paper describes the complete genome sequences of two novel bacteriophages isolated using Streptomyces griseus. Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A.","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/ce141fcb272a85c0445e25ee4917ff4b.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Destructrice produces medium-sized, clear plaques (1.70 ± 0.397 mm), while Rikishi produces smaller, clear plaques (0.83 ± 0.322 mm). Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus phages Destructrice and Rikishi virion and plaque morphology
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as biocontrol agents in the food-processing, agriculture, and aquaculture industries (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two bacteriophages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in nutrient broth (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose, and was incubated for 2 days at 30°C. Two rounds of purification were performed by picking individual plaques and replating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques 1.70 ± 0.997 mm in diameter (n= 86) and Rikishi plaques 0.83 ± 0.322 mm (n=27) (Figure 1). Plaques were measured using the ViralPlaque macro on Fiji (Cacciabue et al., 2019). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a very short (16 ± 2 nm) tail and Rikishi a siphovirus morphology with a long (364 ± 30 nm) tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator (Actino_draft database v578), HHPred (PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases) (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (cluster range = 44859-46511 bp), no identifiable tape measure protein (absent in annotated Streptomyces griseus podovirus phage), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a large genome (cluster range = 126524-133969 bp), a long tape measure protein (6300 bp), and a long terminal repeat (12484 bp). Like other phages in clusters BE2, A, and BD, Rikishi has a DNA primase that is split into two reading frames (Cresawn et al., 2011; Russell and Hatfull, 2017). For both phage, tRNAs identified are also found in a similar location in other phage genomes from the same cluster. No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Bacteriophage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | |
SRA accession no. | ||
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cacciabue M, Currá A, Gismondi MI. 2019. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7: e7729.
","pubmedId":"","doi":"10.7717/peerj.7729"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[{"reviewer":{"displayName":"Dustin Edwards"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"2bd60939-d4dc-447b-8ddf-07778bdea437","decision":"revise","abstract":"This paper describes the complete genome sequences of two novel bacteriophages isolated using Streptomyces griseus. Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A.","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/20fb555345413bd14fb81d8d0af375fa.jpeg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Black arrows indicate plaques for each bacteriophage. Destructrice produces medium-sized, clear plaques (1.70 ± 0.397 mm), while Rikishi produces smaller, clear plaques (0.83 ± 0.322 mm). Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus phages Destructrice and Rikishi virion and plaque morphology
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as biocontrol agents in the food-processing, agriculture, and aquaculture industries (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two bacteriophages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in nutrient broth (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose, and was incubated for 2 days at 30°C. Two rounds of purification were performed by picking individual plaques and replating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques 1.70 ± 0.997 mm in diameter (n= 86) and Rikishi plaques 0.83 ± 0.322 mm (n=27) (Figure 1). Plaques were measured using the ViralPlaque macro on Fiji (Cacciabue et al., 2019). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a very short (16 ± 2 nm) tail and Rikishi a siphovirus morphology with a long (364 ± 30 nm) tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator (Actino_draft database v578), HHPred (PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases) (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (cluster range = 44859-46511 bp), no identifiable tape measure protein (absent in annotated Streptomyces griseus podovirus phage), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a large genome (cluster range = 126524-133969 bp), a long tape measure protein (6300 bp), and a long terminal repeat (12484 bp). Like other phages in clusters BE2, A, and BD, Rikishi has a DNA primase that is split into two reading frames (Cresawn et al., 2011; Russell and Hatfull, 2017). For both phage, tRNAs identified are also found in a similar location in other phage genomes from the same cluster. No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Bacteriophage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | |
SRA accession no. | ||
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cacciabue M, Currá A, Gismondi MI. 2019. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7: e7729.
","pubmedId":"","doi":"10.7717/peerj.7729"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[],"curatorReviews":[]},{"id":"25fe50f4-9db5-461f-9b25-4322b3d3ea21","decision":"accept","abstract":"This paper describes the complete genome sequences of two novel bacteriophages isolated using Streptomyces griseus. Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A.","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/5dad7018e4e6bae9b43d4c457b258438.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Black arrows indicate plaques for each bacteriophage. Destructrice produces medium-sized, clear plaques (1.70 ± 0.397 mm), while Rikishi produces smaller, clear plaques (0.83 ± 0.322 mm). Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus phages Destructrice and Rikishi virion and plaque morphology
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as biocontrol agents in the food-processing, agriculture, and aquaculture industries (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two bacteriophages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in nutrient broth (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose, and was incubated for 2 days at 30°C. Two rounds of purification were performed by picking individual plaques and replating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques 1.70 ± 0.997 mm in diameter (n= 86) and Rikishi plaques 0.83 ± 0.322 mm (n=27) (Figure 1). Plaques were measured using the ViralPlaque macro on Fiji (Cacciabue et al., 2019). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a very short (16 ± 2 nm) tail and Rikishi a siphovirus morphology with a long (364 ± 30 nm) tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator (Actino_draft database v578), HHPred (PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases) (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (cluster range = 44859-46511 bp), no identifiable tape measure protein (absent in annotated Streptomyces griseus podovirus phage), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a large genome (cluster range = 126524-133969 bp), a long tape measure protein (6300 bp), and a long terminal repeat (12484 bp). Like other phages in clusters BE2, A, and BD, Rikishi has a DNA primase that is split into two reading frames (Cresawn et al., 2011; Russell and Hatfull, 2017). For both phage, tRNAs identified are also found in a similar location in other phage genomes from the same cluster. No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Bacteriophage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | |
SRA accession no. | ||
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cacciabue M, Currá A, Gismondi MI. 2019. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7: e7729.
","pubmedId":"","doi":"10.7717/peerj.7729"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[],"curatorReviews":[]},{"id":"7e70c101-ee96-4345-939d-54fff0ff3463","decision":"publish","abstract":"This paper describes the complete genome sequences of two novel bacteriophages isolated using Streptomyces griseus. Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.
","acknowledgements":"We thank the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, the University of Evansville Biology Department, Daniel French, Nick Buechlein, and members of the UE 2024 Phage Discovery Class. We also thank John Andersland and Western Kentucky University for providing electron microscopy imaging with the support of grant P20GM103436-22 (KY INBRE) from the National Institute of General Medical Sciences, National Institutes of Health.
","authors":[{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","project","supervision","writing_reviewEditing","writing_originalDraft"],"email":"ap96@evansville.edu","firstName":"Elizabeth A.","lastName":"Powell","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft","writing_reviewEditing"],"email":"aw680@evansville.edu","firstName":"Allison O.","lastName":"Wortman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","writing_originalDraft","writing_reviewEditing","investigation"],"email":"kt206@evansville.edu","firstName":"Kathryn E.","lastName":"Tyler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ka253@evansville.edu","firstName":"Karina","lastName":"Alfonso-Perez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"gb182@evansville.edu","firstName":"Giselle A.","lastName":"Bez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cb538@evansville.edu","firstName":"Caroline R.","lastName":"Buechlein","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["Northwest Nazarene University, Nampa, Idaho, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"md329@evansville.edu","firstName":"Michael D.","lastName":"Day","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_originalDraft"],"email":"td153@evansville.edu","firstName":"Tasline T.","lastName":"Diab","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ih66@evansville.edu","firstName":"Isabella G. ","lastName":"Henderson","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"oi15@evansville.edu","firstName":"Tosin E.","lastName":"Ishola","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"rr211@evansville.edu","firstName":"Ross S.","lastName":"Rider","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"ds376@evansville.edu","firstName":"Dalton N.","lastName":"Seiler","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"cs645@evansville.edu","firstName":"Colin S.","lastName":"Stooksberry","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_originalDraft"],"email":"as1148@evansville.edu","firstName":"Allyson E.","lastName":"Wary","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["University of Evansville, Evansville, Indiana, United States"],"departments":["Biology"],"credit":["project","dataCuration","investigation","supervision"],"email":"jm757@evansville.edu","firstName":"Julie A.","lastName":"Merkle","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/5dad7018e4e6bae9b43d4c457b258438.jpg"},"imageCaption":"Plaques formed by Destructrice (A) and Rikishi (C) on plates spread with Streptomyces griseus. Black arrows indicate plaques for each bacteriophage. Destructrice produces medium-sized, clear plaques (1.70 ± 0.397 mm), while Rikishi produces smaller, clear plaques (0.83 ± 0.322 mm). Transmission electron micrographs of Destructrice (B) and Rikishi (D) stained with 1% uranyl acetate and viewed at 100 kV accelerating potential in a JEOL 1400Plus transmission electron microscope (Western Kentucky University Southern Kentucky Center for Advanced Microscopy). Phage dimensions are provided in Table 1.
","imageTitle":"Streptomyces griseus phages Destructrice and Rikishi virion and plaque morphology
","methods":"","reagents":"","patternDescription":"Lytic phage cocktails have been used to successfully treat antibiotic-resistant bacterial infections in humans and animals (Cristobal-Cueto et al., 2021; Hatfull et al., 2022). They have also been used as biocontrol agents in the food-processing, agriculture, and aquaculture industries (Cristobal-Cueto et al., 2021). To support these applications, isolating and characterizing novel phages that infect different bacterial species can help to diversify the library of known phages. Here we introduce two bacteriophages that infect Streptomyces griseus: Destructrice and Rikishi.
Destructrice and Rikishi were isolated from moist soil samples collected in Kentucky and Illinois in September 2024 (Table 1). Enriched isolation, purification, and amplification were performed using standard protocols (Zorawik et al., 2024). Briefly, soil samples were suspended in nutrient broth (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose. Soil suspensions were centrifuged, the supernatant was filtered (0.22-µm filter) and the filtrate seeded with Streptomyces griseus (ATCC 10137) and incubated for 3 days at 20°C. The resulting enriched culture was filtered, and the filtrate plated with Streptomyces griseus onto nutrient agar (Research Products International) supplemented with MgCl2, Ca(NO3)2, and dextrose, and was incubated for 2 days at 30°C. Two rounds of purification were performed by picking individual plaques and replating, after which a high-titer lysate was prepared. Destructrice and Rikishi both produced clear plaques, with Destructrice plaques 1.70 ± 0.997 mm in diameter (n= 86) and Rikishi plaques 0.83 ± 0.322 mm (n=27) (Figure 1). Plaques were measured using the ViralPlaque macro on Fiji (Cacciabue et al., 2019). Negative-stain transmission electron microscopy using 1% uranyl acetate showed that Destructrice has a podovirus morphology with a very short (16 ± 2 nm) tail and Rikishi a siphovirus morphology with a long (364 ± 30 nm) tail (Figure 1, Table 1).
Phage genomic DNA was extracted from phage lysates using the Promega Wizard DNA cleanup kit. Phages were prepared for sequencing using the NEBNext Ultra II FS library preparation kit and were sequenced using the Illumina NextSeq 1000 (XLAP-P1 kit) with 100-base, single-end reads. Raw reads were trimmed with Cutadapt 4.7 (using the option: -nextseq-trim30) and filtered with Skewer 0.2.2 (using the options: -q 20 -Q 30 -n -1 50) prior to assembly (Martin, 2011; Jiang et al., 2014). Sequences were then assembled using Newbler v2.9 (Margulies et al., 2005) and Unicycler (Wick et al. 2017), and genome completeness and termini were evaluated using Consed v29 (Gordon et al., 1998; Russell, 2018). Sequencing and genome information is summarized in Table 1. Based on gene content similarity of above 35% to phages in the Actinobacteriophage database (https://phagesdb.org/), Destructrice was assigned to cluster BF and Rikishi was placed in subcluster BE2 (Pope et al., 2017; Hatfull, 2020).
Genomes were autoannotated using DNAMaster v5.23.6 (Pope and Jacobs-Sera, 2018) with Glimmer v3.02b (Delcher et al., 2007) and Genemark v4.28 (Besemer and Borodovsky, 2005). Gene calls were refined using Phamerator v589 (Cresawn et al., 2011), Starterator v589 (http://phages.wustl.edu/starterator/), and BLASTp, using the Actinobacteriophage and NCBI non-redundant database (Altschul et al., 1990), according to criteria outlined in the SEA-Phages Phage Genomics Guide (https://genomicsguide.seaphages.org/). Protein functions were determined using BLASTp, Phamerator (Actino_draft database v578), HHPred (PDB_mmCIF70, Pfam-v.36, UniProt-SwissProt-Viral70_3, and NCBI Conserved Domains databases) (Söding et al., 2005; Zimmerman et al., 2018) and Deep TMHMM v1.0 (Hallgren et al., 2022). tRNAs and tmRNAs were identified using Aragorn v1.2.41 (Laslett and Canback, 2004) and tRNAscanSE v2.0 (Lowe and Eddy, 1997). Default settings were used for all software.
Destructrice encodes 63 predicted protein-coding genes and a cassette of 21 tRNAs. Like other cluster BF phages, Destructrice has a small genome (cluster range = 44859-46511 bp), no identifiable tape measure protein (absent in annotated Streptomyces griseus podovirus phage), and a short terminal repeat (265 bp). Rikishi has 245 protein-coding genes, 42 tRNAs, and 1 tmRNA. Like other BE2 cluster phages, Rikishi has a large genome (cluster range = 126524-133969 bp), a long tape measure protein (6300 bp), and a long terminal repeat (12484 bp). Like other phages in clusters BE2, A, and BD, Rikishi has a DNA primase that is split into two reading frames (Cresawn et al., 2011; Russell and Hatfull, 2017). For both phage, tRNAs identified are also found in a similar location in other phage genomes from the same cluster. No integrase or immunity repressor functions were identified in either genome, suggesting lytic life cycles.
Data Availability
Destructrice is available at GenBank with Accession No. PX234433 and Sequence Read Archive (SRA) No. SRX28484007. Rikishi is available at GenBank with Accession No. PV876926 and Sequence Read Archive (SRA) No. SRX28484029.
TABLE 1: Properties of Streptomyces phages Destructrice and Rikishi.
Bacteriophage | Destructrice | Rikishi |
Location found | Louisville, Kentucky | Albion, Illinois |
Location coordinates | 38.20882 N, 85.75387 W | 38.43662 N, 88.07433 W |
Capsid diameter [nm ± SD (n)] | 63 ± 3 nm (n=5) | 85 ± 12 nm (n=5) |
Tail length [nm ± SD (n)] | 16 ± 2 nm (n=5) | 364 ± 30 nm (n=5) |
Genome size (bp) | 45548 | 132567 |
Approximate coverage (x) | 4540 | 1582 |
Number of reads | 2.9 M | 1.9 M |
GC content (%) | 59.80% | 49.40% |
Direct terminal repeat length | 265 | 12484 |
Cluster | BF | BE2 |
Number of protein coding genes | 63 | 245 |
Number of tRNAs | 21 tRNAs | 42 tRNAs and 1 tmRNA |
GenBank accession no. | PX234433 | |
SRA accession no. | ||
Isolated by | K. Tyler and P. Koche | D. Seiler and D. Wolfe |
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cacciabue M, Currá A, Gismondi MI. 2019. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 7: e7729.
","pubmedId":"","doi":"10.7717/peerj.7729"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Cristobal-Cueto P, García-Quintanilla A, Esteban J, García-Quintanilla M. 2021. Phages in Food Industry Biocontrol and Bioremediation. Antibiotics 10: 786.
","pubmedId":"","doi":"10.3390/antibiotics10070786"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications. Annual Review of Virology 7: 37-61.
","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Hatfull GF, Dedrick RM, Schooley RT. 2022. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annual Review of Medicine 73: 197-211.
","pubmedId":"","doi":"10.1146/annurev-med-080219-122208"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15: 10.1186/1471-2105-15-182.
","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence. Nucleic Acids Research 25: 955-964.
","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al., Rothberg. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
","pubmedId":"","doi":"10.1038/nature03959"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10.
","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero-Bustamante CA, Jacobs-Sera D, Montgomery MT, et al., Hatfull. 2017. Bacteriophages of\n Gordonia\n spp. Display a Spectrum of Diversity and Genetic Relationships. mBio 8: 10.1128/mbio.01069-17.
","pubmedId":"","doi":"10.1128/mBio.01069-17"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database. Bioinformatics 33: 784-786.
","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595.
","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al., Alva. 2018. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. Journal of Molecular Biology 430: 2237-2243.
","pubmedId":"","doi":"10.1016/j.jmb.2017.12.007"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol 2793: 273-298.
","pubmedId":"38526736","doi":""}],"title":"Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi
","reviews":[],"curatorReviews":[]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aegorhinus vitulus","label":"Aegorhinus vitulus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alaimidae","label":"Alaimidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"allobates femoralis","label":"Allobates femoralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alnus glutinosa","label":"Alnus glutinosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa aestivalis","label":"Alosa aestivalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa pseudoharengus","label":"Alosa pseudoharengus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alternaria alternata","label":"Alternaria alternata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"amynthas agrestis","label":"Amynthas Agrestis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma caninum","label":"Ancylostoma caninum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma ceylanicum","label":"Ancylostoma ceylanicum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anemone multifida","label":"Anemone multifida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anguilla rostrata","label":"Anguilla rostrata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anisakis simplex","label":"Anisakis simplex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anomala albopilosa","label":"Anomala albopilosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arabidopsis","label":"Arabidopsis","imageSrc":"arabidopsis.png","imageAlt":"Arabidopsis graphic by Zoe Zorn CC BY 4.0","mod":"TAIR","modLink":"https://arabidopsis.org","linkVariable":""},{"value":"architeuthis dux","label":"Architeuthis dux","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arion vulgaris","label":"Arion vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"armeria","label":"Armeria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"artemia","label":"Artemia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arthrobacter sp.","label":"Arthrobacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia","label":"Ascaridia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia galli","label":"Ascaridia galli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"asparagopsis taxiformis","label":"Asparagopsis taxiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"astatotilapia burtoni","label":"Astatotilapia burtoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"avena sativa","label":"Avena sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aves","label":"Aves","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus","label":"Bacillus (firmicutes)","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus cereus","label":"Bacillus cereus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus mycoides","label":"Bacillus mycoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus subtilis","label":"Bacillus subtilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus thuringiensis","label":"Bacillus thuringiensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus toyonensis","label":"Bacillus toyonensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus wiedmannii","label":"Bacillus wiedmannii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteria","label":"Bacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteriophage","label":"Bacteriophage","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bactrocera","label":"Bactrocera sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"batrachospermum gelatinosum","label":"Batrachospermum gelatinosum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula lenta","label":"Betula lenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula nigra","label":"Betula nigra","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus dahlbohmii","label":"Bombus dahlbohmii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus terrestris","label":"Bombus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombyx mori","label":"Bombyx mori","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bos taurus","label":"Bos Taurus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brachygobius doriae","label":"Brachygobius doriae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica oleracea","label":"Brassica oleracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica rapa","label":"Brassica rapa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brugia malayi","label":"Brugia malayi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"burkholderia thailandensis","label":"Burkholderia thailandensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"buttiauxella","label":"Buttiauxella","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis brenneri","label":"Caenorhabditis brenneri","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis briggsae","label":"Caenorhabditis briggsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"c. elegans","label":"Caenorhabditis elegans","imageSrc":"c-elegans.jpg","imageAlt":"C. elegans graphic by Zoe Zorn CC BY 4.0","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"caenorhabditis inopinata","label":"Caenorhabditis inopinata","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis japonica","label":"Caenorhabditis japonica","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis nigoni","label":"Caenorhabditis nigoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis remanei","label":"Caenorhabditis remanei","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis tropicalis","label":"Caenorhabditis tropicalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus","label":"Calidifontibacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus erzuremensis","label":"Calidifontibacillus erzuremensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calliphora sp","label":"Calliphora sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caltha sagittata","label":"Caltha sagittata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cambarus latimanus","label":"Cambarus latimanus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"candida albicans","label":"Candida albicans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"canis familiaris","label":"Canis familiaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cannabis sativa","label":"Cannabis sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caretta caretta","label":"Caretta caretta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cassiopea xamachana","label":"Cassiopea xamachana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caulobacter vibrioides","label":"Caulobacter vibrioides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cephalopods","label":"Cephalopoda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cerastium arvense","label":"Cerastium arvense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceriodaphnia","label":"Ceriodaphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceroglossus suturalis","label":"Ceroglossus suturalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chaetoceros","label":"Chaetoceros","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chamaecrista fasciculata","label":"Chamaecrista fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chilicola chalcidiformis","label":"Chilicola chalcidiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chitinimonas","label":"Chitinimonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chlamydomonas reinhardtii","label":"Chlamydomonas reinhardtii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chromobacterium","label":"Chromobacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysemys picta","label":"Chrysemys picta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysoperla rufilabris","label":"Chrysoperla rufilabris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"citrus","label":"Citrus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"clavibacter sp.","label":"Clavibacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"colinus virginianus","label":"Colinus virginianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crassostrea virginica","label":"Crassostrea virginica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crithidia fasciculata","label":"Crithidia fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cutibacterium acnes","label":"Cutibacterium acnes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cyanobacteria","label":"Cyanobacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia","label":"Daphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia pulex","label":"Daphnia pulex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera","label":"Diabrotica virgifera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera virgifera virus 1","label":"Diabrotica virgifera virgifera virus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"d. discoideum","label":"Dictyostelium discoideum","imageSrc":"dicty.png","imageAlt":"D. discoideum","mod":"dictyBase","modLink":"http://dictybase.org","linkVariable":""},{"value":"diptera","label":"Diptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dotocryptus bellicosus","label":"Dotocryptus bellicosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drechmeria coniospora","label":"Drechmeria coniospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drosophila","label":"Drosophila","imageSrc":"drosophila.png","imageAlt":"Drosophila graphic by Zoe Zorn CC BY 4.0","mod":"FlyBase","modLink":"https://flybase.org/doi/","linkVariable":"doi"},{"value":"dryopteris campyloptera","label":"Dryopteris campyloptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris expansa","label":"Dryopteris expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris intermedia","label":"Dryopteris intermedia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dugesia dorotocephala","label":"Dugesia dorotocephala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"elasmobranchii","label":"Elasmobranchii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"embryophyta","label":"Embryophyta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enoploteuthis chunii","label":"Enoploteuthis chunii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterobacter aerogenes","label":"Enterobacter aerogenes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterococcus raffinosus","label":"Enterococcus raffinosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"epichloë coenophiala","label":"Epichloë coenophiala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"equus caballus","label":"Equus caballus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erigeron sp","label":"Erigeron sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eristalis","label":"Eristalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eruca vesicaria","label":"Eruca vesicaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erwinia carotovora","label":"Erwinia carotovora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erythronium americanum","label":"Erythronium americanum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"escherichia coli","label":"Escherichia coli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eukaryota","label":"Eukaryotes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"felis catus","label":"Felis catus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella novicida","label":"Francisella novicida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella tularensis","label":"Francisella tularensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fraxinus americana","label":"Fraxinus americana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fucus distichus","label":"Fucus distichus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fungi","label":"Fungi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gasteropelecus sp.","label":"Gasteropelecus sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"geranium sp","label":"Geranium sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"girardia","label":"Girardia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glaucomys volans","label":"Glaucomys volans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glycine max","label":"Glycine max","imageSrc":"","imageAlt":"","mod":"Soybase","modLink":"https://soybase.org","linkVariable":""},{"value":"glyptemys insculpta","label":"Glyptemys insculpta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gossypium hirsutum","label":"Gossypium hirsutum","imageSrc":"","imageAlt":"","mod":"CottonGen","modLink":"https://www.cottongen.org/","linkVariable":""},{"value":"gromphadorhina portentosa","label":"Gromphadorhina portentosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gryllodes sigillatus","label":"Gryllodes sigillatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"haliotis rufescens","label":"Haliotis rufescens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hepacivirus hominis","label":"Hepatitis C Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"herpes simplex virus type 1","label":"Herpes simplex virus type 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human","label":"Human","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human coronavirus oc43","label":"Human coronavirus OC43","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydra vulgaris","label":"Hydra vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydropsyche sp","label":"Hydropsyche sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hymenoptera","label":"Hymenoptera","imageSrc":"","imageAlt":"","mod":"Hymenoptera Genome Database","modLink":"https://hymenoptera.elsiklab.missouri.edu/","linkVariable":""},{"value":"hypochaeris radicata","label":"Hypochaeris radicata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hypodynerus vespiformis","label":"Hypodynerus vespiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflaviridae","label":"Iflaviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflavuris","label":"Iflavirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ipomoea hederacea","label":"Ipomoea hederacea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera","label":"Ischnomera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera ruficollis","label":"Ischnomera ruficollis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"julidochromis marlieri","label":"Julidochromis marlieri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"juniperus virginiana","label":"Juniperus virginiana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"kluyveromyces marxianus","label":"Kluyveromyces marxianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"l. casei","label":"L. casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lacticaseibacillus casei","label":"Lacticaseibacillus casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"larentiinae sp","label":"Larentiinae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"laurus nobilis","label":"Laurus nobilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lepidoptera","label":"Lepidoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"leucanthemum vulgare","label":"Leucanthemum vulgare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"linepithema humile","label":"Linepithema humile","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"liometopum occidentale","label":"Liometopum occidentale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lolium arundinaceum","label":"Lolium arundinaceum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbriculus variegatus","label":"Lumbriculus variegatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbricus terrestris","label":"Lumbricus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lupinus polyphyllus","label":"Lupinus polyphyllus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lycorma delicatula","label":"Lycorma delicatula","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lynx rufus","label":"Lynx rufus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"magnaporthe oryzae","label":"Magnaporthe oryzae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mammalia","label":"Mammalia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"manihot esculenta","label":"Manihot esculenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"medicago lupulina","label":"Medicago lupulina","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"meloidogyne","label":"Meloidogyne","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mimus polyglottos","label":"Mimus polyglottos","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bryophyta","label":"Mosses","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mouse","label":"Mouse","imageSrc":"","imageAlt":"","mod":"MGI","modLink":"https://informatics.jax.org","linkVariable":""},{"value":"m. minutoides","label":"Mus minutoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mycobacterium smegmatis","label":"Mycobacterium smegmatis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nakaseomyces glabratus","label":"Nakaseomyces glabratus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nauphoeta cinerea","label":"Nauphoeta cinerea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"neurospora","label":"Neurospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"n. benthamiana","label":"Nicotiana benthamiana","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/Nicotiana_benthamiana/genome","linkVariable":""},{"value":"nicotiana tabacum","label":"Nicotiana tabacum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae","label":"Noctuidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae sp","label":"Noctuidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nothobranchius furzeri","label":"Nothobranchius furzeri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"onchocerca volvulus","label":"Onchocerca volvulus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"orconectes virilis","label":"Orconectes virilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ormia ochracea","label":"Ormia ochracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"o. sativa","label":"Oryza sativa","imageSrc":"","imageAlt":"","mod":"Gramene","modLink":"https://www.gramene.org/","linkVariable":""},{"value":"other","label":"Other","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"oxalis enneaphylla","label":"Oxalis enneaphylla","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea","label":"Pantoea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea agglomerans","label":"Pantoea agglomerans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"papaver sp","label":"Papaver sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paramecium bursaria","label":"Paramecium bursaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"partitiviridae","label":"Partitiviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pelodiscus sinensis","label":"Pelodiscus sinensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"perezia recurvata","label":"Perezia recurvata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"petromyzon marinus","label":"Petromyzon marinus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis","label":"Photinus pyralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis associated partiti-like virus","label":"Photinus pyralis associated partiti-like virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis iflavirus 1","label":"Photinus pyralis iflavirus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"physcomitrium patens","label":"Physcomitrium patens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus strobus","label":"Pinus strobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus taeda","label":"Pinus taeda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"platycheirus","label":"Platycheirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"plectus sambesii","label":"Plectus sambesii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pogonomyrmex occidentalis","label":"Pogonomyrmex occidentalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"poncirus trifoliata","label":"Poncirus trifoliata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"populus deltoides","label":"Populus deltoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"potato virus y","label":"Potato virus Y","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"primula magellanica","label":"Primula magellanica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pristionchus pacificus","label":"Pristionchus pacificus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"prunus persica","label":"Prunus persica","imageSrc":"","imageAlt":"","mod":"Genome Database for Rosaceae","modLink":"https://www.rosaceae.org/","linkVariable":""},{"value":"psalmopoeus iriminia","label":"Psalmopoeus iriminia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudanabaena sp.","label":"Pseudanabaena sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas","label":"Pseudomonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas aeruginosa","label":"Pseudomonas aeruginosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas glycinae","label":"Pseudomonas glycinae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas putida","label":"Pseudomonas putida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas syringae","label":"Pseudomonas syringae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pterophyllum scalare","label":"Pterophyllum scalare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"python regius","label":"Python regius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"quercus macrocarpa","label":"Quercus macrocarpa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ralstonia solanacearum","label":"Ralstonia solanacearum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranitomeya imitator","label":"Ranitomeya imitator","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranunculus peduncularis","label":"Ranunculus peduncularis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"rat","label":"Rat","imageSrc":"","imageAlt":"","mod":"RGD","modLink":"https://rgd.mcw.edu","linkVariable":""},{"value":"rheinheimera","label":"Rheinheimera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ribes rubrum","label":"Ribes rubrum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"sars-cov-2","label":"SARS-CoV-2","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. cerevisiae","label":"Saccharomyces cerevisiae","imageSrc":"yeast.png","imageAlt":"Yeast graphic by Zoe Zorn CC BY 4.0","mod":"SGD","modLink":"https://yeastgenome.org","linkVariable":""},{"value":"saccharomyces paradoxus","label":"Saccharomyces paradoxus ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. uvarum","label":"Saccharomyces uvarum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schistosoma","label":"Schistosoma","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schizosaccharomyces japonicus","label":"Schizosaccharomyces japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. pombe","label":"Schizosaccharomyces pombe","imageSrc":"pombe.png","imageAlt":"Pombe graphic by Zoe Zorn © Caltech","mod":"PomBase","modLink":"https://www.pombase.org/reference/PMID:","linkVariable":"pmId"},{"value":"schmidtea mediterranea","label":"Schmidtea mediterranea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"senecio sp","label":"Senecio sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"simocephalus","label":"Simocephalus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"siraitia grosvenorii","label":"Siraitia grosvenorii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"solanum lycopersicum","label":"Solanum lycopersicum","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/1/view/","linkVariable":""},{"value":"sorghum","label":"Sorghum","imageSrc":"","imageAlt":"","mod":"SorghumBase","modLink":"https://www.sorghumbase.org","linkVariable":""},{"value":"spiroplasma eriocheiris","label":"Spiroplasma eriocheiris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus aureus","label":"Staphylococcus aureus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus epidermidis","label":"Staphylococcus epidermidis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"steinernema carpocapsae","label":"Steinernema carpocapsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"steinernema hermaphroditum","label":"Steinernema hermaphroditum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stenotrophomonas geniculata","label":"Stenotrophomonas geniculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus gordonii ","label":"Streptococcus gordonii ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus mutans","label":"Streptococcus mutans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":" streptococcus pneumoniae","label":"Streptococcus pneumoniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. purpuratus","label":"Strongylocentrotus purpuratus","imageSrc":"","imageAlt":"","mod":"Echinobase","modLink":"https://www.echinobase.org","linkVariable":""},{"value":"strongyloides ratti","label":"Strongyloides ratti","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"sulfolobus","label":"Sulfolobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"symphoricarpos albus","label":"Symphoricarpos albus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syncirsodes","label":"Syncirsodes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"synechococcus elongatus","label":"Synechococcus elongatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syrphidae","label":"Syrphidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tarantobelus jeffdanielsi","label":"Tarantobelus jeffdanielsi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"taraxacum officinale","label":"Taraxacum officinale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tatochila theodice","label":"Tatochila theodice","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetrahymena","label":"Tetrahymena","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetramorium immigrans","label":"Tetramorium immigrans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tomato brown rugose fruit virus","label":"ToBRFV","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trachemys scripta","label":"Trachemys scripta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tribolium castaneum","label":"Tribolium castaneum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichoptera","label":"Trichoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichuris muris","label":"Trichuris muris","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"trifolium repens","label":"Trifolium repens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trypoxylus dichotomus","label":"Trypoxylus dichotomus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tsuga canadensis","label":"Tsuga canadensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ulva expansa","label":"Ulva expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"universal","label":"Universal","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"vargula hilgendorfii","label":"Vargula hilgendorfii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"vespula vulgaris","label":"Vespula vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"virus","label":"Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"watasenia scintillans","label":"Watasenia scintillans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"wolbachia pipientis","label":"Wolbachia pipientis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"xenopus","label":"Xenopus","imageSrc":"xenopus.png","imageAlt":"Xenopus graphic by Zoe Zorn CC BY 4.0","mod":"XenBase","modLink":"https://xenbase.org","linkVariable":""},{"value":"xenorhabdus griffiniae","label":"Xenorhabdus griffiniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"yramea cytheris","label":"Yramea cytheris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zaprionus indianus","label":"Zaprionus indianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zea mays","label":"Zea mays","imageSrc":"","imageAlt":"","mod":"MaizeGDB","modLink":"https://www.maizegdb.org","linkVariable":""},{"value":"zebrafish","label":"Zebrafish","imageSrc":"zebrafish.png","imageAlt":"Zebrafish graphic by Zoe Zorn CC BY 4.0","mod":"ZFIN","modLink":"https://zfin.org","linkVariable":""}]}},"pageContext":{"id":"ae6d0bed-3fed-491f-a6ce-3b89d1d8176a","citedBy":[],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}