Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis a B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Madison.Rosales@my.utsa.edu","firstName":"Madison","lastName":"Rosales","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Andrea.Lozano3@my.utsa.edu","firstName":"Andrea","lastName":"Lozano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Katey.Stoddard@my.utsa.edu","firstName":"Katey","lastName":"Stoddard","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Benjamin.Neuman@my.utsa.edu","firstName":"Benjamin","lastName":"Neuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Sofia.Sanchez@my.utsa.edu","firstName":"Sofia","lastName":"Sanchez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Miguel.Bernal@my.utsa.edu","firstName":"Miguel","lastName":"Bernal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Halle.Brown@my.utsa.edu","firstName":"Halle","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Mia.Enciso@my.utsa.edu","firstName":"Mia","lastName":"Enciso","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"James.Hunter2@my.utsa.edu","firstName":"James","lastName":"Hunter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Ryan.Le@my.utsa.edu","firstName":"Ryan","lastName":"Le","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Faye.Selesi@my.utsa.edu","firstName":"Faye","lastName":"Selesi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"kristina.vaquera@my.utsa.edu","firstName":"Kristina","lastName":"Vaquera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Martin.Villarreal@my.utsa.edu","firstName":"Martin","lastName":"Villarreal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft","writing_reviewEditing","conceptualization","project","supervision"],"email":"nicholas.young@utsa.edu","firstName":"Nicholas","lastName":"Young","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0000-1764-2147"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/4a14b10e3ed9da8e967cc77f28deb03a.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate.
","imageTitle":"Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis a B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022), was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
","reviews":[],"curatorReviews":[]},{"id":"2c73cc61-084d-4c69-abc1-4325473c7cbd","decision":"revise","abstract":"Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis a B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Madison.Rosales@my.utsa.edu","firstName":"Madison","lastName":"Rosales","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Andrea.Lozano3@my.utsa.edu","firstName":"Andrea","lastName":"Lozano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Katey.Stoddard@my.utsa.edu","firstName":"Katey","lastName":"Stoddard","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Benjamin.Neuman@my.utsa.edu","firstName":"Benjamin","lastName":"Neuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Sofia.Sanchez@my.utsa.edu","firstName":"Sofia","lastName":"Sanchez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Miguel.Bernal@my.utsa.edu","firstName":"Miguel","lastName":"Bernal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Halle.Brown@my.utsa.edu","firstName":"Halle","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Mia.Enciso@my.utsa.edu","firstName":"Mia","lastName":"Enciso","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"James.Hunter2@my.utsa.edu","firstName":"James","lastName":"Hunter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Ryan.Le@my.utsa.edu","firstName":"Ryan","lastName":"Le","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Faye.Selesi@my.utsa.edu","firstName":"Faye","lastName":"Selesi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the 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","dataTable":null,"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/2265359e011a78873c12955442010e06.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate.
","imageTitle":"Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis a B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022), was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
","reviews":[{"reviewer":{"displayName":"Jamie Wallen"},"openAcknowledgement":false,"status":{"submitted":true}},{"reviewer":{"displayName":"Tom D'Elia"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"772ba001-8254-447e-ba3c-c9628d5fd76f","decision":"revise","abstract":"Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis a B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Madison.Rosales@my.utsa.edu","firstName":"Madison","lastName":"Rosales","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Andrea.Lozano3@my.utsa.edu","firstName":"Andrea","lastName":"Lozano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Katey.Stoddard@my.utsa.edu","firstName":"Katey","lastName":"Stoddard","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Benjamin.Neuman@my.utsa.edu","firstName":"Benjamin","lastName":"Neuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Sofia.Sanchez@my.utsa.edu","firstName":"Sofia","lastName":"Sanchez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Miguel.Bernal@my.utsa.edu","firstName":"Miguel","lastName":"Bernal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Halle.Brown@my.utsa.edu","firstName":"Halle","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Mia.Enciso@my.utsa.edu","firstName":"Mia","lastName":"Enciso","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"James.Hunter2@my.utsa.edu","firstName":"James","lastName":"Hunter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Ryan.Le@my.utsa.edu","firstName":"Ryan","lastName":"Le","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Faye.Selesi@my.utsa.edu","firstName":"Faye","lastName":"Selesi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"kristina.vaquera@my.utsa.edu","firstName":"Kristina","lastName":"Vaquera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Martin.Villarreal@my.utsa.edu","firstName":"Martin","lastName":"Villarreal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft","writing_reviewEditing","conceptualization","project","supervision"],"email":"nicholas.young@utsa.edu","firstName":"Nicholas","lastName":"Young","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0000-1764-2147"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/2265359e011a78873c12955442010e06.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate using an Arthrobacter globiformis lawn.
","imageTitle":"Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022) was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
","reviews":[],"curatorReviews":[]},{"id":"25df66e7-c125-4630-b332-8ff1e2160ad0","decision":"accept","abstract":"Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the 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San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the 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US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"kristina.vaquera@my.utsa.edu","firstName":"Kristina","lastName":"Vaquera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Martin.Villarreal@my.utsa.edu","firstName":"Martin","lastName":"Villarreal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft","writing_reviewEditing","conceptualization","project","supervision"],"email":"nicholas.young@utsa.edu","firstName":"Nicholas","lastName":"Young","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0000-1764-2147"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/2265359e011a78873c12955442010e06.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate using an Arthrobacter globiformis lawn.
","imageTitle":"Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022) was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
","reviews":[],"curatorReviews":[]},{"id":"bf5eaea5-f20e-4d1c-bb03-a460f2ec57f8","decision":"edit","abstract":"Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Madison.Rosales@my.utsa.edu","firstName":"Madison","lastName":"Rosales","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Andrea.Lozano3@my.utsa.edu","firstName":"Andrea","lastName":"Lozano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Katey.Stoddard@my.utsa.edu","firstName":"Katey","lastName":"Stoddard","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Benjamin.Neuman@my.utsa.edu","firstName":"Benjamin","lastName":"Neuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Sofia.Sanchez@my.utsa.edu","firstName":"Sofia","lastName":"Sanchez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Miguel.Bernal@my.utsa.edu","firstName":"Miguel","lastName":"Bernal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Halle.Brown@my.utsa.edu","firstName":"Halle","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Mia.Enciso@my.utsa.edu","firstName":"Mia","lastName":"Enciso","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"James.Hunter2@my.utsa.edu","firstName":"James","lastName":"Hunter","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Ryan.Le@my.utsa.edu","firstName":"Ryan","lastName":"Le","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Faye.Selesi@my.utsa.edu","firstName":"Faye","lastName":"Selesi","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"kristina.vaquera@my.utsa.edu","firstName":"Kristina","lastName":"Vaquera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Martin.Villarreal@my.utsa.edu","firstName":"Martin","lastName":"Villarreal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft","writing_reviewEditing","conceptualization","project","supervision"],"email":"nicholas.young@utsa.edu","firstName":"Nicholas","lastName":"Young","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0000-1764-2147"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/2265359e011a78873c12955442010e06.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate using an Arthrobacter globiformis lawn.
","imageTitle":"Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022) was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
","reviews":[],"curatorReviews":[]},{"id":"040352dc-f384-44b7-807f-2032d07d9bc5","decision":"publish","abstract":"Bacteriophage KNG13, a siphovirus, was isolated in San Antonio, Texas, USA, using Arthrobacter globiformis B-2979. KNG13 has a genome length of 15,768-bp and is assigned to actinobacteriophage cluster FE based on gene content.
","acknowledgements":"We would like to thank the Department of Biology, Health, and the Environment at The University of Texas at San Antonio for providing the means to conduct this research and show KNG13 to the world. We would also like to thank the SEA-PHAGES program for training and continued support throughout the process of bacteriophage discovery and bioinformatics.
","authors":[{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Kelci.Grahmann@my.utsa.edu","firstName":"Kelci","lastName":"Grahmann","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Chance.Cecchine@my.utsa.edu","firstName":"Chance","lastName":"Cecchine","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Madison.Rosales@my.utsa.edu","firstName":"Madison","lastName":"Rosales","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Andrea.Lozano3@my.utsa.edu","firstName":"Andrea","lastName":"Lozano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Katey.Stoddard@my.utsa.edu","firstName":"Katey","lastName":"Stoddard","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Francene.Wang@my.utsa.edu","firstName":"Francene","lastName":"Wang","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Nicholas.Long2@my.utsa.edu","firstName":"Nicholas","lastName":"Long","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Benjamin.Neuman@my.utsa.edu","firstName":"Benjamin","lastName":"Neuman","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Sofia.Sanchez@my.utsa.edu","firstName":"Sofia","lastName":"Sanchez","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Miguel.Bernal@my.utsa.edu","firstName":"Miguel","lastName":"Bernal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Halle.Brown@my.utsa.edu","firstName":"Halle","lastName":"Brown","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Mia.Enciso@my.utsa.edu","firstName":"Mia","lastName":"Enciso","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the 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US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Danielle.Toscano@my.utsa.edu","firstName":"Danielle","lastName":"Toscano","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Joseph.Urrabazo@my.utsa.edu","firstName":"Joseph","lastName":"Urrabazo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"kristina.vaquera@my.utsa.edu","firstName":"Kristina","lastName":"Vaquera","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft"],"email":"Martin.Villarreal@my.utsa.edu","firstName":"Martin","lastName":"Villarreal","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["The University of Texas at San Antonio, San Antonio, TX, US"],"departments":["Biology, Health, and the Environment"],"credit":["writing_originalDraft","writing_reviewEditing","conceptualization","project","supervision"],"email":"nicholas.young@utsa.edu","firstName":"Nicholas","lastName":"Young","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0009-0000-1764-2147"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was funded by the department of Biology, Health, and the Environment at The University of Texas at San Antonio.
","image":{"url":"https://portal.micropublication.org/uploads/2265359e011a78873c12955442010e06.jpg"},"imageCaption":"Clear, circular plaques of KNG13 on a 100 mm PYCa agar plate using an Arthrobacter globiformis lawn.
","imageTitle":"
Plaque morphology of KNG13
","methods":"","reagents":"","patternDescription":"Bacteriophages are incredibly abundant and diverse, with multitude of applications ranging from phage therapy to biotechnology (Dedrick et al., 2019; Naureen et al., 2020; Rogovski et al., 2021). Here, we describe the isolation and characterization of a novel bacteriophage, KNG13.
Phage KNG13 was extracted from mildly damp soil collected on a trail in San Antonio, Texas, USA (29.663765 N, 98.421426 W) when the ambient temperature was approximately 27°C. The soil sample was processed using standard protocols (Zorawik et al., 2024). Briefly, approximately 7 cm3 of soil sample was suspended in 10 ml PYCa (peptone, yeast extract, calcium chloride, and dextrose) liquid medium and agitated in a shaking incubator for 2 hours. The suspension was then spun (2,000 x g for 10 minutes) and the supernatant filtered using a syringe filter (0.2-micron pore size). The filtrate was subsequently plated in PYCa top agar with Arthrobacter globiformis B-2979 and plates incubated at 30 ˚C for 48 hours. Phage KNG13, which forms plaques that are clear and approximately 1.5 mm in diameter (Figure 1), was purified by two rounds of selecting plaques and plating.
A lysate for KNG13 was prepared (2.8 x 109 PFU/mL) and used to extract DNA with the Promega Wizard DNA kit. Phage DNA was then prepared for sequencing with the NEB Ultra FS kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit), yielding 1,345,255 single-end 100 base reads. Raw sequencing reads were trimmed using cutadapt v4.7 (using the option: –nextseq-trim 30) and subsequently filtered with skewer v0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly. The genome was assembled using Newbler v.29 (Miller et al., 2010) and checked for completeness using Consed v2.9 (Gordon et al., 1998), resulting in an assembled genome of 15,768 base pairs with 7,815-fold coverage. The genome consisted of 67.6 % GC content, with 3’ single-stranded overhangs of a 5’CCACGTATACCGTCC.
The genome was annotated with DNA Master v5.23.6 (cobamide2.bio.pitt.edu) and PECAAN v20250130 (discover.kbrinsgd.org) (Rinehart et al., 2016), using Glimmer v3.02 (Delcher et al. 2007 ) and GeneMark v2.5p (Besemer and Borodovsky 2005) to predict genes and Starterator v605 (http://phages.wustl.edu/starterator/) to refine start coordinates. Putative gene functions were assigned using Phamerator v593 (Cresawn et al., 2011), HHPred (Söding 2005) searches against the the PDB_mmCIF70, Pfam- v.36, NCBI Conserved Domains databases and NCBI Blastp v2.16.0 (Altschul et al. 1990) searches against the Actinobacteriophage and NCBI non-redundant databases. DeepTMHMM v1.0.42 (Hallgren et al. 2022) was used to identify transmembrane domains and tRNAscanSE 2.0 (Lowe & Eddy 1997) to identify tRNAs. All software were used with default settings.
Based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, KNG13 was assigned to actinobacteriophage cluster FE (Pope et al., 2017; Russell & Hatfull, 2016). A total of 26 putative genes were identified, of which 13 could be assigned putative functions. These include several functions related to virion structure and assembly, an endolysin, two proteins with DNA-binding domains, one HNH endonuclease, and a RepA-like replication initiator. Consistent with cluster FE phages, the gene encoding the endolysin is adjacent to two genes that encode transmembrane domains, one of which is assigned as a holin in a subset of phages. The RepA-like replication initiator protein of KNG13 is grouped in a protein family with members only encoded in 4 other FE phages, to date. No lysogeny-related functions could be identified, suggesting KNG13 is unlikely to establish lysogeny.
Nucleotide sequence accession numbers
KNG13 is available at GenBank with Accession No. PV876960 and Sequence Read Archive (SRA) No. SRX31241838.
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool.","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.","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.","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Dedrick RM, Guerrero Bustamante CA, Garlena RA, Russell DA, Ford K, Harris K, et al., Spencer H. 2019. Engineered Bacteriophages for Treatment of a Patient with a Disseminated drug-resistant Mycobacterium Abscessus.","pubmedId":"","doi":"10.1038/s41591-019-0437-z"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer.","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing.","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.","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Hatfull GF. 2020. Actinobacteriophages: Genomics, Dynamics, and Applications.","pubmedId":"","doi":"10.1146/annurev-virology-122019-070009"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.","pubmedId":"","doi":"10.1186/1471-2105-15-182"},{"reference":"Lowe TM, Eddy SR. 1997. tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence.","pubmedId":"","doi":"10.1093/nar/25.5.955"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.","pubmedId":"","doi":"10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data.","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, et al., Bertelli M. 2020. Bacteriophages presence in nature and their role in the natural selection of bacterial populations.","pubmedId":"","doi":"10.23750/abm.v91i13-S.10819"},{"reference":"Pittsburgh Bacteriophage Institute. 2010. Cluster FE Phages.","pubmedId":"","doi":""},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships.","pubmedId":"","doi":"10.1128/mbio.01069-17"},{"reference":"Rinehart C, Gaffney B, Wood J, Smith S. 2016. PECAAN, a Phage Evidence Collection And Annotation Network.","pubmedId":"","doi":""},{"reference":"Rogovski P, Cadamuro RD, Da Silva R, De Souza EB, Bonatto C, Viancelli A, et al., Fongaro G. 2021. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators.","pubmedId":"","doi":"10.3389/fmicb.2021.793135"},{"reference":"Russell DA, Hatfull GF. 2016. PhagesDB: the actinobacteriophage database.","pubmedId":"","doi":"10.1093/bioinformatics/btw711"},{"reference":"Science Education Alliance. . Phage Discovery Guide.","pubmedId":"","doi":""},{"reference":"Sharp R. 2001. Bacteriophages: biology and history.","pubmedId":"","doi":"10.1002/jctb.434"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction.","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Wetzel KS, Aull HG, Zack KM, Garlena RA, Hatfull GF. 2020. Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages.","pubmedId":"","doi":"10.1128/mBio.00385-20"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","pubmedId":"","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts.","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequence of Arthrobacter Phage KNG13
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