A key mutation for generating transgenics in Tribolium castaneum is vermilionwhite (vw). vw is a deletion that removes most of the vermilion locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the Tribolium homolog of norpA. The vw deletion is 4434 bps. The deletion eliminates not onlyvermilion but also gustatory receptor candidate 58 and norpA function. Therefore, the vermilionwhite (vw) mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency vermilionwhite,(Df) vw.
","acknowledgements":"","authors":[{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["formalAnalysis","methodology","investigation","writing_originalDraft","writing_reviewEditing","dataCuration"],"email":"jojose@iu.edu","firstName":"Josy ","lastName":"Joseph","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0009-0006-2105-9580"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Center for Genomics and Bioinformatics"],"credit":["dataCuration","formalAnalysis","methodology","writing_reviewEditing"],"email":"drusch@iu.edu","firstName":"Douglas","lastName":"Rusch","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0000-0002-1066-2687"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["conceptualization","fundingAcquisition","investigation","supervision","writing_originalDraft","writing_reviewEditing"],"email":"azelhof@iu.edu","firstName":"Andrew","lastName":"Zelhof","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"000000017085822X"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":null,"extendedData":[],"funding":"This work was supported by the National Science Foundation (IOS-1928781) to A.C.Z.
","image":{"url":"https://portal.micropublication.org/uploads/a99e0cc418cb7ffffab95930da8ee25e.png"},"imageCaption":"A. Schematic of Tribolium castaneum genetic loci of three genes affected by vermilionwhite (vw) deletion. B. Coverage or depth of sequence alignment at genomic region specific to the vw deletion. Thirty nucleotides flanking each side of the 5′ and 3′ deletion breakpoints are highlighted, with red lines indicating the exact deletion boundaries. C. The amino acid sequence of exon 9 of norpA and the new open reading frame amino acids of exon 9 in vw. There is a stop codon after 15 amino acids. D. Comparison of protein structure of Phospholipase C between norpA and truncated norpA reveals the PH domain, Phosphoinositide phospholipase C beta1-4-like EF-hand domain and Phosphatidylinositol-specific phospholipase C domains remain intact but the C2 domain is truncated.
","imageTitle":"Genomic organization in the vw deletion
","methods":"Tribolium lines and husbandry: All animals were raised at 28oC on a standard flour yeast mix. The following strains were utilized: vermilionwhite (vw), and a heterozygote of vermilionwhite (vw) (Lorenzen et al., 2002a) and Lucifer (Lu) (Haas & Beeman, 2012).
Sequencing and genome assembly: 40 < 1 day old vermilionwhite (vw) and Lucifer (Lu) heterozygote pupae were isolated and immediately frozen in liquid nitrogen and stored at –80oC. Pupae were shipped on dry ice to Psomagen (https://www.psomagen.com/) for processing. DNA extraction, library construction, and PacBio sequencing were all performed by Psomagen. The PacBio hifi reads were assembled with hifiasm (v0.25.0-r726) (Cheng et al., 2024; Cheng et al., 2021; Cheng et al., 2022). The resulting assemblies as well as the input reads were mapped to the reference genome Tribolium castaneum strain GA2 (v1.1) using minimap2 (v2.28) (Li, 2018) with default parameters. This identified a 4434 bp deletion. Among reads that span the deleted region, we identified 139 reads without the deletion and 149 reads that contain the deletion. The sequencing reads have been deposited in the SRA database and have the following accession numbers: SRR37271882 : wild-type vermilion locus reads and SRR37271883 : vw deletion locus reads.
norpA protein structure: The protein domains were compiled using InterPro (Blum et al., 2025).
","reagents":"","patternDescription":"Tribolium is a widely utilized model organism for evolutionary and developmental biology questions and understanding regulatory mechanisms for agricultural pests (Adamski et al., 2019; Brown et al., 2009; Pointer et al., 2021; Rosner et al., 2020). Tribolium was the first Coleoptera genome to be sequenced (Tribolium Genome Sequence Consortium 2008 -(Tribolium Genome Sequencing et al., 2008)), and an updated genome sequence based upon long read sequencing (icTriCast1.1 - Childers et al., 2021) is now available. Tribolium is amenable to both forward and reverse genetics, and in particular transgenesis is well established (Campbell et al., 2022; Klingler & Bucher, 2022). For transgenics, the 3XP3 fluorescent marked transposable elements is an efficient marker (Berghammer et al., 1999; Horn et al., 2000) and easily detected in Tribolium mutant retinas that lack pigmentation, e.g. pearl, platinum and white. Lorenzen et al. demonstrated that the Tribolium white mutation (Eddleman & Bell, 1963) is a null mutation of the Tribolium homolog of vermilion (Lorenzen et al., 2002a). Moreover, given the absence of pigment in vermilion mutant retinas, a set of transposable elements have been generated that result in the expression of vermilion and thus restores pigmentation to the retina (Lorenzen et al., 2002b). As a result, most of if not all Tribolium transgenics are generated in the vw mutant background.
The initial characterization of vermilionwhite demonstrated that the mutant is a deletion that removes the first five exons and extends into the last sixth exon of vermilion (Figure 1A). The upstream breakpoint was not mapped. To map the upstream breakpoint, we took advantage of PacBio long read sequence that contained the vw mutation. Our sequencing revealed a 4434 bp deletion. The sequence confirmed the break point that lies within vermilion and identified theupstream second breakpoint (Figure 1B). The deletion eliminates the entire gustatory receptor candidate 58 locus and extends into the Tribolium norpA locus. norpA encodes a Phospholipase C which is critical for phototransduction and in its absence vision is disrupted ((Bloomquist et al., 1988)). The deletion results in a 3’ prime deletion of exon 9 of the norpA locus resulting in the truncation of the C2 domain of the phospholipase and an addition of 15 unrelated amino acids Figure 1C,D). The C2 domain is 91 amino-acid residues and thought to be involved in calcium-dependent phospholipid binding and membrane targeting (Davletov & Sudhof, 1993). The loss of the C2 domain can have multiple effects. It can prevent the protein from binding to the lipid bilayers (Croessmann et al., 2018) or it can impair the protein’s ability to respond to the calcium signals (Corbalan-Garcia & Gomez-Fernandez, 2014). The truncation can also reduce the stability of the protein, leading to premature degradation (Buetow & Huang, 2016). Thus the truncation of the C2 domain would suggest that the mutated norpA allele in the vw mutation is a loss of function allele.
With respect to the generation of transgenics, one will need to account for the additional mutations in vw but this concern can be alleviated using CRISPR/Cas9 generated vermilion alleles (Adrianos et al., 2018; Markley et al., 2024). Whereas the existence of two additional mutations may decrease the usefulness of vw with respect to transgenics, the existence of defined deletions has been critical for mapping of genes and confirming the nature of alleles. Moreover, the vw mutation now adds a key mutation to the toolbox of understanding sensory perception. The uncovering of the norpA mutation can now help define the dynamics of phototransduction in Tribolium and permit an investigation in the role of vision in Tribolium behaviors, e.g. circadian rhythms. Overall due to the elimination of two other loci we propose that the vwmutation is now referred as Deficiency vermilionwhite ,(Df) vw.
","references":[{"reference":"
Adamski, Z., Bufo, S. A., Chowanski, S., Falabella, P., Lubawy, J., Marciniak, P., Pacholska-Bogalska, J., Salvia, R., Scrano, L., Slocinska, M., Spochacz, M., Szymczak, M., Urbanski, A., Walkowiak-Nowicka, K., & Rosinski, G. (2019). Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies - A Review. Front Physiol, 10, 319. https://doi.org/10.3389/fphys.2019.00319
","pubmedId":"","doi":""},{"reference":"Adrianos, S., Lorenzen, M., & Oppert, B. (2018). Metabolic pathway interruption: CRISPR/Cas9-mediated knockout of tryptophan 2,3-dioxygenase in Tribolium castaneum. J Insect Physiol, 107, 104-109. https://doi.org/10.1016/j.jinsphys.2018.03.004
","pubmedId":"","doi":""},{"reference":"Berghammer, A. J., Klingler, M., & Wimmer, E. A. (1999). A universal marker for transgenic insects. Nature, 402(6760), 370-371. https://doi.org/10.1038/46463
","pubmedId":"","doi":""},{"reference":"Bloomquist, B. T., Shortridge, R. D., Schneuwly, S., Perdew, M., Montell, C., Steller, H., Rubin, G., & Pak, W. L. (1988). Isolation of a putative phospholipase C gene of Drosophila, norpA, and its role in phototransduction. Cell, 54(5), 723-733. https://doi.org/10.1016/s0092-8674(88)80017-5
","pubmedId":"","doi":""},{"reference":"Blum, M., Andreeva, A., Florentino, L. C., Chuguransky, S. R., Grego, T., Hobbs, E., Pinto, B. L., Orr, A., Paysan-Lafosse, T., Ponamareva, I., Salazar, G. A., Bordin, N., Bork, P., Bridge, A., Colwell, L., Gough, J., Haft, D. H., Letunic, I., Llinares-Lopez, F., . . . Bateman, A. (2025). InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res, 53(D1), D444-D456. https://doi.org/10.1093/nar/gkae1082
","pubmedId":"","doi":""},{"reference":"Brown, S. J., Shippy, T. D., Miller, S., Bolognesi, R., Beeman, R. W., Lorenzen, M. D., Bucher, G., Wimmer, E. A., & Klingler, M. (2009). The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology. Cold Spring Harb Protoc, 2009(8), pdb emo126. https://doi.org/10.1101/pdb.emo126
","pubmedId":"","doi":""},{"reference":"Buetow, L., & Huang, D. T. (2016). Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nat Rev Mol Cell Biol, 17(10), 626-642. https://doi.org/10.1038/nrm.2016.91 \t
","pubmedId":"","doi":""},{"reference":"Campbell, J. F., Athanassiou, C. G., Hagstrum, D. W., & Zhu, K. Y. (2022). Tribolium castaneum: A Model Insect for Fundamental and Applied Research. Annu Rev Entomol, 67, 347-365. https://doi.org/10.1146/annurev-ento-080921-075157 \t
","pubmedId":"","doi":""},{"reference":"Cheng, H., Asri, M., Lucas, J., Koren, S., & Li, H. (2024). Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21(6), 967-970. https://doi.org/10.1038/s41592-024-02269-8
","pubmedId":"","doi":""},{"reference":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021). Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18(2), 170-175. https://doi.org/10.1038/s41592-020-01056-5
","pubmedId":"","doi":""},{"reference":"Cheng, H., Jarvis, E. D., Fedrigo, O., Koepfli, K. P., Urban, L., Gemmell, N. J., & Li, H. (2022). Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol, 40(9), 1332-1335. https://doi.org/10.1038/s41587-022-01261-x
","pubmedId":"","doi":""},{"reference":"Childers, A. K., Geib, S. M., Sim, S. B., Poelchau, M. F., Coates, B. S., Simmonds, T. J., Scully, E. D., Smith, T. P. L., Childers, C. P., Corpuz, R. L., Hackett, K., & Scheffler, B. (2021). The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects, 12(7). https://doi.org/10.3390/insects12070626
","pubmedId":"","doi":""},{"reference":"Corbalan-Garcia, S., & Gomez-Fernandez, J. C. (2014). Signaling through C2 domains: more than one lipid target. Biochim Biophys Acta, 1838(6), 1536-1547. https://doi.org/10.1016/j.bbamem.2014.01.008
","pubmedId":"","doi":""},{"reference":"Croessmann, S., Sheehan, J. H., Lee, K. M., Sliwoski, G., He, J., Nagy, R., Riddle, D., Mayer, I. A., Balko, J. M., Lanman, R., Miller, V. A., Cantley, L. C., Meiler, J., & Arteaga, C. L. (2018). PIK3CA C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3Kalpha Inhibitors. Clin Cancer Res, 24(6), 1426-1435. https://doi.org/10.1158/1078-0432.CCR-17-2141
","pubmedId":"","doi":""},{"reference":"Davletov, B. A., & Sudhof, T. C. (1993). A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J Biol Chem, 268(35), 26386-26390. https://www.ncbi.nlm.nih.gov/pubmed/8253763
","pubmedId":"","doi":""},{"reference":"Eddleman, H. L., & Bell, A. E. (1963). Four new eye-color mutants in Tribolium castaneum (Abstr.). Genetics, 48, 888.
","pubmedId":"","doi":""},{"reference":"Haas, M. S., & Beeman, R. W. (2012). Coming apart at the seams: morphological evidence for pregnathal head capsule borders in adult Tribolium castaneum. Dev Genes Evol, 222(2), 99-111. https://doi.org/10.1007/s00427-012-0397-5
","pubmedId":"","doi":""},{"reference":"Horn, C., Jaunich, B., & Wimmer, E. A. (2000). Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Dev Genes Evol, 210(12), 623-629. https://doi.org/10.1007/s004270000111
","pubmedId":"","doi":""},{"reference":"Klingler, M., & Bucher, G. (2022). The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. Evodevo, 13(1), 14. https://doi.org/10.1186/s13227-022-00201-9
","pubmedId":"","doi":""},{"reference":"Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100. https://doi.org/10.1093/bioinformatics/bty191
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Transgene expression from the Tribolium castaneum Polyubiquitin promoter. Insect Mol Biol, 11(5), 399-407. https://doi.org/10.1046/j.1365-2583.2002.00349.x
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Cloning and characterization of the Tribolium castaneum eye-color genes encoding tryptophan oxygenase and kynurenine 3-monooxygenase. Genetics, 160(1), 225-234. https://doi.org/10.1093/genetics/160.1.225
","pubmedId":"","doi":""},{"reference":"Markley, H. C., Helms, K. J., Maar, M., Zentner, G. E., Wade, M. J., & Zelhof, A. C. (2024). Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. J Insect Sci, 24(4). https://doi.org/10.1093/jisesa/ieae082
","pubmedId":"","doi":""},{"reference":"Pointer, M. D., Gage, M. J. G., & Spurgin, L. G. (2021). Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb), 126(6), 869-883. https://doi.org/10.1038/s41437-021-00420-1
","pubmedId":"","doi":""},{"reference":"Rosner, J., Wellmeyer, B., & Merzendorfer, H. (2020). Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance. Curr Pharm Des, 26(29), 3554-3568. https://doi.org/10.2174/1381612826666200513113140
","pubmedId":"","doi":""},{"reference":"Tribolium Genome Sequencing, C., Richards, S., Gibbs, R. A., Weinstock, G. M., Brown, S. J., Denell, R., Beeman, R. W., Gibbs, R., Beeman, R. W., Brown, S. J., Bucher, G., Friedrich, M., Grimmelikhuijzen, C. J., Klingler, M., Lorenzen, M., Richards, S., Roth, S., Schroder, R., Tautz, D., . . . Bucher, G. (2008). The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190), 949-955. https://doi.org/10.1038/nature06784
","pubmedId":"","doi":""}],"title":"Defining the breakpoints of the vermilion white (vw) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA.
","reviews":[{"reviewer":{"displayName":"Yoshinori Tomoyasu"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"83631c47-473d-433e-b4da-578fbe049893","decision":"accept","abstract":"A key mutation for generating transgenics in Tribolium castaneum is vermilionwhite (vw). vw is a deletion that removes most of the vermilion locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the Tribolium homolog of norpA. The vw deletion is 4434 bps. The deletion eliminates not only vermilion but also gustatory receptor candidate 58 and norpA function. Therefore, the vw mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency vermilionwhite, Df (vw).
","acknowledgements":"","authors":[{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["formalAnalysis","methodology","investigation","writing_originalDraft","writing_reviewEditing","dataCuration"],"email":"jojose@iu.edu","firstName":"Josy ","lastName":"Joseph","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0009-0006-2105-9580"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Center for Genomics and Bioinformatics"],"credit":["dataCuration","formalAnalysis","methodology","writing_reviewEditing"],"email":"drusch@iu.edu","firstName":"Douglas","lastName":"Rusch","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0000-0002-1066-2687"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["conceptualization","fundingAcquisition","investigation","supervision","writing_originalDraft","writing_reviewEditing"],"email":"azelhof@iu.edu","firstName":"Andrew","lastName":"Zelhof","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"000000017085822X"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was supported by the National Science Foundation (IOS-1928781) to A.C.Z.
","image":{"url":"https://portal.micropublication.org/uploads/649e43ef0be738136f8ff21bc459674b.png"},"imageCaption":"A. Schematic of Tribolium castaneum genetic loci of three genes affected by vermilionwhite (vw) deletion. B. Coverage or depth of sequence alignment at genomic region specific to the vw deletion. Thirty nucleotides flanking each side of the 5′ and 3′ deletion breakpoints are highlighted, with red lines indicating the exact deletion boundaries. C. The amino acid sequence of exon 9 of norpA and the new open reading frame amino acids of exon 9 in vw. There is a stop codon after 15 amino acids. D. Comparison of protein structure of Phospholipase C between norpA and truncated norpA reveals the PH domain, Phosphoinositide phospholipase C beta1-4-like EF-hand domain and Phosphatidylinositol-specific phospholipase C domains remain intact but the C2 domain is truncated.
","imageTitle":"Genomic organization of the vw deletion
","methods":"Tribolium lines and husbandry: All animals were raised at 28oC on a standard flour yeast mix. The following strains were utilized: vermilionwhite (vw), and a strain heterozygous for vermilionwhite (vw) (Lorenzen et al., 2002a) and Lucifer (Lu) (Haas & Beeman, 2012).
Sequencing and genome assembly: 40 < 1 day old vermilionwhite (vw) and Lucifer (Lu) heterozygote pupae were isolated and immediately frozen in liquid nitrogen and stored at –80oC. Pupae were shipped on dry ice to Psomagen (https://www.psomagen.com/) for processing. DNA extraction, library construction, and PacBio sequencing were all performed by Psomagen. The PacBio hifi reads were assembled with hifiasm (v0.25.0-r726) (Cheng et al., 2024; Cheng et al., 2021; Cheng et al., 2022). The resulting assemblies as well as the input reads were mapped to the reference genome Tribolium castaneum strain icTriCast1.1 using minimap2 (v2.28) (Li, 2018) with default parameters. This identified a 4434 bp deletion. Among reads that span the deleted region, we identified 139 reads without the deletion and 149 reads that contain the deletion. The sequencing reads have been deposited in the SRA database and have the following accession numbers: SRR37271882 : wild-type vermilion locus reads and SRR37271883 : vw deletion locus reads.
norpA protein structure: The protein domains were compiled using InterPro (Blum et al., 2025).
","reagents":"","patternDescription":"Tribolium is a widely utilized model organism for evolutionary and developmental biology questions and understanding regulatory mechanisms for agricultural pests (Adamski et al., 2019; Brown et al., 2009; Pointer et al., 2021; Rosner et al., 2020). Tribolium was the first Coleoptera genome to be sequenced (Tribolium Genome Sequencing Consortium, 2008), and an updated genome sequence based upon long read sequencing (icTriCast1.1 - (Childers et al., 2021) is now available. Tribolium is amenable to both forward and reverse genetics, and in particular transgenesis is well established (Campbell et al., 2022; Klingler & Bucher, 2022). For transgenics, the 3XP3 fluorescent marked transposable elements is an efficient marker (Berghammer et al., 1999; Horn et al., 2000) and easily detected in Tribolium mutant retinas that lack pigmentation, e.g. pearl, platinum and white. Lorenzen et al. demonstrated that the Tribolium white mutation (Eddleman & Bell, 1963) is a null mutation of the Tribolium homolog of vermilion (Lorenzen et al., 2002a). Moreover, given the absence of pigment in vermilion mutant retinas, a set of transposable elements have been generated that result in the expression of vermilion and thus restores pigmentation to the retina (Lorenzen et al., 2002b). As a result, many Tribolium transgenics are generated in the vw mutant background.
The initial characterization of vermilionwhite demonstrated that the mutant is a deletion that removes the first five exons and extends into the last sixth exon of vermilion (Figure 1A). The upstream breakpoint was not mapped. To map the upstream breakpoint, we took advantage of PacBio long read sequence that contained the vw mutation. Our sequencing revealed a 4,434 bp deletion. The sequence confirmed the break point that lies within vermilion and identified theupstream second breakpoint (Figure 1B). The deletion eliminates the entire gustatory receptor candidate 58 locus and extends into the Tribolium norpA locus. norpA encodes a Phospholipase C which is critical for phototransduction and in its absence vision is disrupted (Bloomquist et al., 1988). The deletion results in a 3’ prime deletion of exon 9 of the norpA locus resulting in the truncation of the C2 domain of the phospholipase and an addition of 15 unrelated amino acids Figure 1C,D). The C2 domain is 91 amino-acid residues and thought to be involved in calcium-dependent phospholipid binding and membrane targeting (Davletov & Sudhof, 1993). The loss of the C2 domain can have multiple effects. It can prevent the protein from binding to the lipid bilayers (Croessmann et al., 2018) or it can impair the protein’s ability to respond to the calcium signals (Corbalan-Garcia & Gomez-Fernandez, 2014). The truncation can also reduce the stability of the protein, leading to premature degradation (Buetow & Huang, 2016). Thus the truncation of the C2 domain would suggest that the mutated norpA allele in the vw mutation is a loss of function allele.
With respect to the generation of transgenics, one will need to account for the additional mutations in vw but this concern can be alleviated using CRISPR/Cas9 generated vermilion alleles (Adrianos et al., 2018; Markley et al., 2024). Whereas the existence of two additional mutations may decrease the usefulness of vw with respect to transgenics, the existence of defined deletions has been critical for mapping of genes and confirming the nature of alleles. Moreover, the vw mutation now adds a key mutation to the toolbox of understanding sensory perception. The uncovering of the norpA mutation can now help define the dynamics of phototransduction in Tribolium and permit an investigation in the role of vision in Tribolium behaviors, e.g. circadian rhythms. Overall due to the elimination of two other loci we propose that the vwmutation is now referred as Deficiency vermilionwhite , Df (vw).
","references":[{"reference":"
Adamski, Z., Bufo, S. A., Chowanski, S., Falabella, P., Lubawy, J., Marciniak, P., Pacholska-Bogalska, J., Salvia, R., Scrano, L., Slocinska, M., Spochacz, M., Szymczak, M., Urbanski, A., Walkowiak-Nowicka, K., & Rosinski, G. (2019). Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies - A Review. Front Physiol, 10, 319. https://doi.org/10.3389/fphys.2019.00319
","pubmedId":"","doi":""},{"reference":"Adrianos, S., Lorenzen, M., & Oppert, B. (2018). Metabolic pathway interruption: CRISPR/Cas9-mediated knockout of tryptophan 2,3-dioxygenase in Tribolium castaneum. J Insect Physiol, 107, 104-109. https://doi.org/10.1016/j.jinsphys.2018.03.004
","pubmedId":"","doi":""},{"reference":"Berghammer, A. J., Klingler, M., & Wimmer, E. A. (1999). A universal marker for transgenic insects. Nature, 402(6760), 370-371. https://doi.org/10.1038/46463
","pubmedId":"","doi":""},{"reference":"Bloomquist, B. T., Shortridge, R. D., Schneuwly, S., Perdew, M., Montell, C., Steller, H., Rubin, G., & Pak, W. L. (1988). Isolation of a putative phospholipase C gene of Drosophila, norpA, and its role in phototransduction. Cell, 54(5), 723-733. https://doi.org/10.1016/s0092-8674(88)80017-5
","pubmedId":"","doi":""},{"reference":"Blum, M., Andreeva, A., Florentino, L. C., Chuguransky, S. R., Grego, T., Hobbs, E., Pinto, B. L., Orr, A., Paysan-Lafosse, T., Ponamareva, I., Salazar, G. A., Bordin, N., Bork, P., Bridge, A., Colwell, L., Gough, J., Haft, D. H., Letunic, I., Llinares-Lopez, F., . . . Bateman, A. (2025). InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res, 53(D1), D444-D456. https://doi.org/10.1093/nar/gkae1082
","pubmedId":"","doi":""},{"reference":"Brown, S. J., Shippy, T. D., Miller, S., Bolognesi, R., Beeman, R. W., Lorenzen, M. D., Bucher, G., Wimmer, E. A., & Klingler, M. (2009). The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology. Cold Spring Harb Protoc, 2009(8), pdb emo126. https://doi.org/10.1101/pdb.emo126
","pubmedId":"","doi":""},{"reference":"Buetow, L., & Huang, D. T. (2016). Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nat Rev Mol Cell Biol, 17(10), 626-642. https://doi.org/10.1038/nrm.2016.91 \t
","pubmedId":"","doi":""},{"reference":"Campbell, J. F., Athanassiou, C. G., Hagstrum, D. W., & Zhu, K. Y. (2022). Tribolium castaneum: A Model Insect for Fundamental and Applied Research. Annu Rev Entomol, 67, 347-365. https://doi.org/10.1146/annurev-ento-080921-075157 \t
","pubmedId":"","doi":""},{"reference":"Cheng, H., Asri, M., Lucas, J., Koren, S., & Li, H. (2024). Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21(6), 967-970. https://doi.org/10.1038/s41592-024-02269-8
","pubmedId":"","doi":""},{"reference":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021). Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18(2), 170-175. https://doi.org/10.1038/s41592-020-01056-5
","pubmedId":"","doi":""},{"reference":"Cheng, H., Jarvis, E. D., Fedrigo, O., Koepfli, K. P., Urban, L., Gemmell, N. J., & Li, H. (2022). Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol, 40(9), 1332-1335. https://doi.org/10.1038/s41587-022-01261-x
","pubmedId":"","doi":""},{"reference":"Childers, A. K., Geib, S. M., Sim, S. B., Poelchau, M. F., Coates, B. S., Simmonds, T. J., Scully, E. D., Smith, T. P. L., Childers, C. P., Corpuz, R. L., Hackett, K., & Scheffler, B. (2021). The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects, 12(7). https://doi.org/10.3390/insects12070626
","pubmedId":"","doi":""},{"reference":"Corbalan-Garcia, S., & Gomez-Fernandez, J. C. (2014). Signaling through C2 domains: more than one lipid target. Biochim Biophys Acta, 1838(6), 1536-1547. https://doi.org/10.1016/j.bbamem.2014.01.008
","pubmedId":"","doi":""},{"reference":"Croessmann, S., Sheehan, J. H., Lee, K. M., Sliwoski, G., He, J., Nagy, R., Riddle, D., Mayer, I. A., Balko, J. M., Lanman, R., Miller, V. A., Cantley, L. C., Meiler, J., & Arteaga, C. L. (2018). PIK3CA C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3Kalpha Inhibitors. Clin Cancer Res, 24(6), 1426-1435. https://doi.org/10.1158/1078-0432.CCR-17-2141
","pubmedId":"","doi":""},{"reference":"Davletov, B. A., & Sudhof, T. C. (1993). A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J Biol Chem, 268(35), 26386-26390. https://www.ncbi.nlm.nih.gov/pubmed/8253763
","pubmedId":"","doi":""},{"reference":"Eddleman, H. L., & Bell, A. E. (1963). Four new eye-color mutants in Tribolium castaneum (Abstr.). Genetics, 48, 888.
","pubmedId":"","doi":""},{"reference":"Haas, M. S., & Beeman, R. W. (2012). Coming apart at the seams: morphological evidence for pregnathal head capsule borders in adult Tribolium castaneum. Dev Genes Evol, 222(2), 99-111. https://doi.org/10.1007/s00427-012-0397-5
","pubmedId":"","doi":""},{"reference":"Horn, C., Jaunich, B., & Wimmer, E. A. (2000). Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Dev Genes Evol, 210(12), 623-629. https://doi.org/10.1007/s004270000111
","pubmedId":"","doi":""},{"reference":"Klingler, M., & Bucher, G. (2022). The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. Evodevo, 13(1), 14. https://doi.org/10.1186/s13227-022-00201-9
","pubmedId":"","doi":""},{"reference":"Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100. https://doi.org/10.1093/bioinformatics/bty191
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Transgene expression from the Tribolium castaneum Polyubiquitin promoter. Insect Mol Biol, 11(5), 399-407. https://doi.org/10.1046/j.1365-2583.2002.00349.x
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Cloning and characterization of the Tribolium castaneum eye-color genes encoding tryptophan oxygenase and kynurenine 3-monooxygenase. Genetics, 160(1), 225-234. https://doi.org/10.1093/genetics/160.1.225
","pubmedId":"","doi":""},{"reference":"Markley, H. C., Helms, K. J., Maar, M., Zentner, G. E., Wade, M. J., & Zelhof, A. C. (2024). Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. J Insect Sci, 24(4). https://doi.org/10.1093/jisesa/ieae082
","pubmedId":"","doi":""},{"reference":"Pointer, M. D., Gage, M. J. G., & Spurgin, L. G. (2021). Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb), 126(6), 869-883. https://doi.org/10.1038/s41437-021-00420-1
","pubmedId":"","doi":""},{"reference":"Rosner, J., Wellmeyer, B., & Merzendorfer, H. (2020). Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance. Curr Pharm Des, 26(29), 3554-3568. https://doi.org/10.2174/1381612826666200513113140
","pubmedId":"","doi":""},{"reference":"Tribolium Genome Sequencing Consortium, (2008). The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190), 949-955. https://doi.org/10.1038/nature06784
","pubmedId":"","doi":""}],"title":"Defining the breakpoints of the vermilion white (vw) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA.
","reviews":[],"curatorReviews":[]},{"id":"3036286e-ae9f-4c57-be97-c662339c2b51","decision":"edit","abstract":"A key mutation for generating transgenics in Tribolium castaneum is vermilionwhite (vw). vw is a deletion that removes most of the vermilion locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the Tribolium homolog of norpA. The vw deletion is 4434 bps. The deletion eliminates not only vermilion but also gustatory receptor candidate 58 and norpA function. Therefore, the vw mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency vermilionwhite, Df (vw).
","acknowledgements":"","authors":[{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["formalAnalysis","methodology","investigation","writing_originalDraft","writing_reviewEditing","dataCuration"],"email":"jojose@iu.edu","firstName":"Josy ","lastName":"Joseph","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0009-0006-2105-9580"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Center for Genomics and Bioinformatics"],"credit":["dataCuration","formalAnalysis","methodology","writing_reviewEditing"],"email":"drusch@iu.edu","firstName":"Douglas","lastName":"Rusch","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0000-0002-1066-2687"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["conceptualization","fundingAcquisition","investigation","supervision","writing_originalDraft","writing_reviewEditing"],"email":"azelhof@iu.edu","firstName":"Andrew","lastName":"Zelhof","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"000000017085822X"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was supported by the National Science Foundation (IOS-1928781) to A.C.Z.
","image":{"url":"https://portal.micropublication.org/uploads/bf400e18706985db65b2d376b99e85e4.png"},"imageCaption":"A. Schematic of Tribolium castaneum genetic loci of three genes affected by vermilionwhite (vw) deletion. B. Coverage or depth of sequence alignment at genomic region specific to the vw deletion. Thirty nucleotides flanking each side of the 5′ and 3′ deletion breakpoints are highlighted, with red lines indicating the exact deletion boundaries. C. The amino acid sequence of exon 9 of norpA and the new open reading frame amino acids of exon 9 in vw. There is a stop codon after 15 amino acids. D. Comparison of protein structure of Phospholipase C between norpA and truncated norpA reveals the PH domain, Phosphoinositide phospholipase C beta1-4-like EF-hand domain and Phosphatidylinositol-specific phospholipase C domains remain intact but the C2 domain is truncated.
","imageTitle":"Genomic organization of the vw deletion
","methods":"Tribolium lines and husbandry: All animals were raised at 28oC on a standard flour yeast mix. The following strains were utilized: vermilionwhite (vw), and a strain heterozygous for vermilionwhite (vw) (Lorenzen et al., 2002a) and Lucifer (Lu) (Haas & Beeman, 2012).
Sequencing and genome assembly: 40 < 1 day old vermilionwhite (vw) and Lucifer (Lu) heterozygote pupae were isolated and immediately frozen in liquid nitrogen and stored at –80oC. Pupae were shipped on dry ice to Psomagen (https://www.psomagen.com/) for processing. DNA extraction, library construction, and PacBio sequencing were all performed by Psomagen. The PacBio hifi reads were assembled with hifiasm (v0.25.0-r726) (Cheng et al., 2024; Cheng et al., 2021; Cheng et al., 2022). The resulting assemblies as well as the input reads were mapped to the reference genome Tribolium castaneum strain icTriCast1.1 using minimap2 (v2.28) (Li, 2018) with default parameters. This identified a 4434 bp deletion. Among reads that span the deleted region, we identified 139 reads without the deletion and 149 reads that contain the deletion. The sequencing reads have been deposited in the SRA database and have the following accession numbers: SRR37271882 : wild-type vermilion locus reads and SRR37271883 : vw deletion locus reads.
norpA protein structure: The protein domains were compiled using InterPro (Blum et al., 2025).
","reagents":"","patternDescription":"Tribolium is a widely utilized model organism for evolutionary and developmental biology questions and understanding regulatory mechanisms for agricultural pests (Adamski et al., 2019; Brown et al., 2009; Pointer et al., 2021; Rosner et al., 2020). Tribolium was the first Coleoptera genome to be sequenced (Tribolium Genome Sequencing Consortium, 2008), and an updated genome sequence based upon long read sequencing (icTriCast1.1 - (Childers et al., 2021) is now available. Tribolium is amenable to both forward and reverse genetics, and in particular transgenesis is well established (Campbell et al., 2022; Klingler & Bucher, 2022). For transgenics, the 3XP3 fluorescent marked transposable elements is an efficient marker (Berghammer et al., 1999; Horn et al., 2000) and easily detected in Tribolium mutant retinas that lack pigmentation, e.g. pearl, platinum and white. Lorenzen et al. demonstrated that the Tribolium white mutation (Eddleman & Bell, 1963) is a null mutation of the Tribolium homolog of vermilion (Lorenzen et al., 2002a). Moreover, given the absence of pigment in vermilion mutant retinas, a set of transposable elements have been generated that result in the expression of vermilion and thus restores pigmentation to the retina (Lorenzen et al., 2002b). As a result, many Tribolium transgenics are generated in the vw mutant background.
The initial characterization of vermilionwhite demonstrated that the mutant is a deletion that removes the first five exons and extends into the last sixth exon of vermilion (Figure 1A). The upstream breakpoint was not mapped. To map the upstream breakpoint, we took advantage of PacBio long read sequence that contained the vw mutation. Our sequencing revealed a 4,434 bp deletion. The sequence confirmed the break point that lies within vermilion and identified the upstream second breakpoint (Figure 1B). The deletion eliminates the entire gustatory receptor candidate 58 locus and extends into the Tribolium norpA locus. norpA encodes a Phospholipase C which is critical for phototransduction and in its absence vision is disrupted (Bloomquist et al., 1988). The deletion results in a 3’ prime deletion of exon 9 of the norpA locus resulting in the truncation of the C2 domain of the phospholipase and an addition of 15 unrelated amino acids Figure 1C,D). The C2 domain is 91 amino-acid residues and thought to be involved in calcium-dependent phospholipid binding and membrane targeting (Davletov & Sudhof, 1993). The loss of the C2 domain can have multiple effects. It can prevent the protein from binding to the lipid bilayers (Croessmann et al., 2018) or it can impair the protein’s ability to respond to the calcium signals (Corbalan-Garcia & Gomez-Fernandez, 2014). The truncation can also reduce the stability of the protein, leading to premature degradation (Buetow & Huang, 2016). Thus the truncation of the C2 domain would suggest that the mutated norpA allele in the vw mutation is a loss of function allele.
With respect to the generation of transgenics, one will need to account for the additional mutations in vw but this concern can be alleviated using CRISPR/Cas9 generated vermilion alleles (Adrianos et al., 2018; Markley et al., 2024). Whereas the existence of two additional mutations may decrease the usefulness of vw with respect to transgenics, the existence of defined deletions has been critical for mapping of genes and confirming the nature of alleles. Moreover, the vw mutation now adds a key mutation to the toolbox of understanding sensory perception. The uncovering of the norpA mutation can now help define the dynamics of phototransduction in Tribolium and permit an investigation in the role of vision in Tribolium behaviors, e.g. circadian rhythms. Overall due to the elimination of two other loci we propose that the vwmutation is now referred as Deficiency vermilionwhite , Df (vw).
","references":[{"reference":"
Adamski, Z., Bufo, S. A., Chowanski, S., Falabella, P., Lubawy, J., Marciniak, P., Pacholska-Bogalska, J., Salvia, R., Scrano, L., Slocinska, M., Spochacz, M., Szymczak, M., Urbanski, A., Walkowiak-Nowicka, K., & Rosinski, G. (2019). Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies - A Review. Front Physiol, 10, 319. https://doi.org/10.3389/fphys.2019.00319
","pubmedId":"","doi":""},{"reference":"Adrianos, S., Lorenzen, M., & Oppert, B. (2018). Metabolic pathway interruption: CRISPR/Cas9-mediated knockout of tryptophan 2,3-dioxygenase in Tribolium castaneum. J Insect Physiol, 107, 104-109. https://doi.org/10.1016/j.jinsphys.2018.03.004
","pubmedId":"","doi":""},{"reference":"Berghammer, A. J., Klingler, M., & Wimmer, E. A. (1999). A universal marker for transgenic insects. Nature, 402(6760), 370-371. https://doi.org/10.1038/46463
","pubmedId":"","doi":""},{"reference":"Bloomquist, B. T., Shortridge, R. D., Schneuwly, S., Perdew, M., Montell, C., Steller, H., Rubin, G., & Pak, W. L. (1988). Isolation of a putative phospholipase C gene of Drosophila, norpA, and its role in phototransduction. Cell, 54(5), 723-733. https://doi.org/10.1016/s0092-8674(88)80017-5
","pubmedId":"","doi":""},{"reference":"Blum, M., Andreeva, A., Florentino, L. C., Chuguransky, S. R., Grego, T., Hobbs, E., Pinto, B. L., Orr, A., Paysan-Lafosse, T., Ponamareva, I., Salazar, G. A., Bordin, N., Bork, P., Bridge, A., Colwell, L., Gough, J., Haft, D. H., Letunic, I., Llinares-Lopez, F., . . . Bateman, A. (2025). InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res, 53(D1), D444-D456. https://doi.org/10.1093/nar/gkae1082
","pubmedId":"","doi":""},{"reference":"Brown, S. J., Shippy, T. D., Miller, S., Bolognesi, R., Beeman, R. W., Lorenzen, M. D., Bucher, G., Wimmer, E. A., & Klingler, M. (2009). The red flour beetle, Tribolium castaneum (Coleoptera): a model for studies of development and pest biology. Cold Spring Harb Protoc, 2009(8), pdb emo126. https://doi.org/10.1101/pdb.emo126
","pubmedId":"","doi":""},{"reference":"Buetow, L., & Huang, D. T. (2016). Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nat Rev Mol Cell Biol, 17(10), 626-642. https://doi.org/10.1038/nrm.2016.91 \t
","pubmedId":"","doi":""},{"reference":"Campbell, J. F., Athanassiou, C. G., Hagstrum, D. W., & Zhu, K. Y. (2022). Tribolium castaneum: A Model Insect for Fundamental and Applied Research. Annu Rev Entomol, 67, 347-365. https://doi.org/10.1146/annurev-ento-080921-075157 \t
","pubmedId":"","doi":""},{"reference":"Cheng, H., Asri, M., Lucas, J., Koren, S., & Li, H. (2024). Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods, 21(6), 967-970. https://doi.org/10.1038/s41592-024-02269-8
","pubmedId":"","doi":""},{"reference":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021). Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 18(2), 170-175. https://doi.org/10.1038/s41592-020-01056-5
","pubmedId":"","doi":""},{"reference":"Cheng, H., Jarvis, E. D., Fedrigo, O., Koepfli, K. P., Urban, L., Gemmell, N. J., & Li, H. (2022). Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol, 40(9), 1332-1335. https://doi.org/10.1038/s41587-022-01261-x
","pubmedId":"","doi":""},{"reference":"Childers, A. K., Geib, S. M., Sim, S. B., Poelchau, M. F., Coates, B. S., Simmonds, T. J., Scully, E. D., Smith, T. P. L., Childers, C. P., Corpuz, R. L., Hackett, K., & Scheffler, B. (2021). The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects, 12(7). https://doi.org/10.3390/insects12070626
","pubmedId":"","doi":""},{"reference":"Corbalan-Garcia, S., & Gomez-Fernandez, J. C. (2014). Signaling through C2 domains: more than one lipid target. Biochim Biophys Acta, 1838(6), 1536-1547. https://doi.org/10.1016/j.bbamem.2014.01.008
","pubmedId":"","doi":""},{"reference":"Croessmann, S., Sheehan, J. H., Lee, K. M., Sliwoski, G., He, J., Nagy, R., Riddle, D., Mayer, I. A., Balko, J. M., Lanman, R., Miller, V. A., Cantley, L. C., Meiler, J., & Arteaga, C. L. (2018). PIK3CA C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3Kalpha Inhibitors. Clin Cancer Res, 24(6), 1426-1435. https://doi.org/10.1158/1078-0432.CCR-17-2141
","pubmedId":"","doi":""},{"reference":"Davletov, B. A., & Sudhof, T. C. (1993). A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J Biol Chem, 268(35), 26386-26390. https://www.ncbi.nlm.nih.gov/pubmed/8253763
","pubmedId":"","doi":""},{"reference":"Eddleman, H. L., & Bell, A. E. (1963). Four new eye-color mutants in Tribolium castaneum (Abstr.). Genetics, 48, 888.
","pubmedId":"","doi":""},{"reference":"Haas, M. S., & Beeman, R. W. (2012). Coming apart at the seams: morphological evidence for pregnathal head capsule borders in adult Tribolium castaneum. Dev Genes Evol, 222(2), 99-111. https://doi.org/10.1007/s00427-012-0397-5
","pubmedId":"","doi":""},{"reference":"Horn, C., Jaunich, B., & Wimmer, E. A. (2000). Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Dev Genes Evol, 210(12), 623-629. https://doi.org/10.1007/s004270000111
","pubmedId":"","doi":""},{"reference":"Klingler, M., & Bucher, G. (2022). The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. Evodevo, 13(1), 14. https://doi.org/10.1186/s13227-022-00201-9
","pubmedId":"","doi":""},{"reference":"Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100. https://doi.org/10.1093/bioinformatics/bty191
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Transgene expression from the Tribolium castaneum Polyubiquitin promoter. Insect Mol Biol, 11(5), 399-407. https://doi.org/10.1046/j.1365-2583.2002.00349.x
","pubmedId":"","doi":""},{"reference":"Lorenzen, M. D., Brown, S. J., Denell, R. E., & Beeman, R. W. (2002). Cloning and characterization of the Tribolium castaneum eye-color genes encoding tryptophan oxygenase and kynurenine 3-monooxygenase. Genetics, 160(1), 225-234. https://doi.org/10.1093/genetics/160.1.225
","pubmedId":"","doi":""},{"reference":"Markley, H. C., Helms, K. J., Maar, M., Zentner, G. E., Wade, M. J., & Zelhof, A. C. (2024). Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. J Insect Sci, 24(4). https://doi.org/10.1093/jisesa/ieae082
","pubmedId":"","doi":""},{"reference":"Pointer, M. D., Gage, M. J. G., & Spurgin, L. G. (2021). Tribolium beetles as a model system in evolution and ecology. Heredity (Edinb), 126(6), 869-883. https://doi.org/10.1038/s41437-021-00420-1
","pubmedId":"","doi":""},{"reference":"Rosner, J., Wellmeyer, B., & Merzendorfer, H. (2020). Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance. Curr Pharm Des, 26(29), 3554-3568. https://doi.org/10.2174/1381612826666200513113140
","pubmedId":"","doi":""},{"reference":"Tribolium Genome Sequencing Consortium, (2008). The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190), 949-955. https://doi.org/10.1038/nature06784
","pubmedId":"","doi":""}],"title":"Defining the breakpoints of the vermilion white (vw) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA.
","reviews":[],"curatorReviews":[]},{"id":"9c21e07d-2673-46a1-b714-592fe8895a94","decision":"accept","abstract":"A key mutation for generating transgenics in Tribolium castaneum is vermilionwhite (vw). vw is a deletion that removes most of the vermilion locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the Tribolium homolog of norpA. The vw deletion is 4434 bps. The deletion eliminates not only vermilion but also gustatory receptor candidate 58 and norpA function. Therefore, the vw mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency vermilionwhite, Df (vw).
","acknowledgements":"","authors":[{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["formalAnalysis","methodology","investigation","writing_originalDraft","writing_reviewEditing","dataCuration"],"email":"jojose@iu.edu","firstName":"Josy ","lastName":"Joseph","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0009-0006-2105-9580"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Center for Genomics and Bioinformatics"],"credit":["dataCuration","formalAnalysis","methodology","writing_reviewEditing"],"email":"drusch@iu.edu","firstName":"Douglas","lastName":"Rusch","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0000-0002-1066-2687"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["conceptualization","fundingAcquisition","investigation","supervision","writing_originalDraft","writing_reviewEditing"],"email":"azelhof@iu.edu","firstName":"Andrew","lastName":"Zelhof","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"000000017085822X"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was supported by the National Science Foundation (IOS-1928781) to A.C.Z.
","image":{"url":"https://portal.micropublication.org/uploads/bf400e18706985db65b2d376b99e85e4.png"},"imageCaption":"A. Schematic of Tribolium castaneum genetic loci of three genes affected by vermilionwhite (vw) deletion. B. Coverage or depth of sequence alignment at genomic region specific to the vw deletion. Thirty nucleotides flanking each side of the 5′ and 3′ deletion breakpoints are highlighted, with red lines indicating the exact deletion boundaries. C. The amino acid sequence of exon 9 of norpA and the new open reading frame amino acids of exon 9 in vw. There is a stop codon after 15 amino acids. D. Comparison of protein structure of Phospholipase C between norpA and truncated norpA reveals the PH domain, Phosphoinositide phospholipase C beta1-4-like EF-hand domain and Phosphatidylinositol-specific phospholipase C domains remain intact but the C2 domain is truncated.
","imageTitle":"Genomic organization of the vw deletion
","methods":"Tribolium lines and husbandry: All animals were raised at 28oC on a standard flour yeast mix. The following strains were utilized: vermilionwhite (vw), and a strain heterozygous for vermilionwhite (vw) (Lorenzen et al., 2002a) and Lucifer (Lu) (Haas & Beeman, 2012).
Sequencing and genome assembly: 40 < 1 day old vermilionwhite (vw) and Lucifer (Lu) heterozygote pupae were isolated and immediately frozen in liquid nitrogen and stored at –80oC. Pupae were shipped on dry ice to Psomagen (https://www.psomagen.com/) for processing. DNA extraction, library construction, and PacBio sequencing were all performed by Psomagen. The PacBio hifi reads were assembled with hifiasm (v0.25.0-r726) (Cheng et al., 2024; Cheng et al., 2021; Cheng et al., 2022). The resulting assemblies as well as the input reads were mapped to the reference genome Tribolium castaneum strain icTriCast1.1 using minimap2 (v2.28) (Li, 2018) with default parameters. This identified a 4434 bp deletion. Among reads that span the deleted region, we identified 139 reads without the deletion and 149 reads that contain the deletion. The sequencing reads have been deposited in the SRA database and have the following accession numbers: SRR37271882 : wild-type vermilion locus reads and SRR37271883 : vw deletion locus reads.
norpA protein structure: The protein domains were compiled using InterPro (Blum et al., 2025).
","reagents":"","patternDescription":"Tribolium is a widely utilized model organism for evolutionary and developmental biology questions and understanding regulatory mechanisms for agricultural pests (Adamski et al., 2019; Brown et al., 2009; Pointer et al., 2021; Rosner et al., 2020). Tribolium was the first Coleoptera genome to be sequenced (Tribolium Genome Sequencing Consortium, 2008), and an updated genome sequence based upon long read sequencing (icTriCast1.1 - (Childers et al., 2021) is now available. Tribolium is amenable to both forward and reverse genetics, and in particular transgenesis is well established (Campbell et al., 2022; Klingler & Bucher, 2022). For transgenics, the 3XP3 fluorescent marked transposable elements is an efficient marker (Berghammer et al., 1999; Horn et al., 2000) and easily detected in Tribolium mutant retinas that lack pigmentation, e.g. pearl, platinum and white. Lorenzen et al. demonstrated that the Tribolium white mutation (Eddleman & Bell, 1963) is a null mutation of the Tribolium homolog of vermilion (Lorenzen et al., 2002a). Moreover, given the absence of pigment in vermilion mutant retinas, a set of transposable elements have been generated that result in the expression of vermilion and thus restores pigmentation to the retina (Lorenzen et al., 2002b). As a result, many Tribolium transgenics are generated in the vw mutant background.
The initial characterization of vermilionwhite demonstrated that the mutant is a deletion that removes the first five exons and extends into the last sixth exon of vermilion (Figure 1A). The upstream breakpoint was not mapped. To map the upstream breakpoint, we took advantage of PacBio long read sequence that contained the vw mutation. Our sequencing revealed a 4,434 bp deletion. The sequence confirmed the break point that lies within vermilion and identified the upstream second breakpoint (Figure 1B). The deletion eliminates the entire gustatory receptor candidate 58 locus and extends into the Tribolium norpA locus. norpA encodes a Phospholipase C which is critical for phototransduction and in its absence vision is disrupted (Bloomquist et al., 1988). The deletion results in a 3’ prime deletion of exon 9 of the norpA locus resulting in the truncation of the C2 domain of the phospholipase and an addition of 15 unrelated amino acids Figure 1C,D). The C2 domain is 91 amino-acid residues and thought to be involved in calcium-dependent phospholipid binding and membrane targeting (Davletov & Sudhof, 1993). The loss of the C2 domain can have multiple effects. It can prevent the protein from binding to the lipid bilayers (Croessmann et al., 2018) or it can impair the protein’s ability to respond to the calcium signals (Corbalan-Garcia & Gomez-Fernandez, 2014). The truncation can also reduce the stability of the protein, leading to premature degradation (Buetow & Huang, 2016). Thus the truncation of the C2 domain would suggest that the mutated norpA allele in the vw mutation is a loss of function allele.
With respect to the generation of transgenics, one will need to account for the additional mutations in vw but this concern can be alleviated using CRISPR/Cas9 generated vermilion alleles (Adrianos et al., 2018; Markley et al., 2024). Whereas the existence of two additional mutations may decrease the usefulness of vw with respect to transgenics, the existence of defined deletions has been critical for mapping of genes and confirming the nature of alleles. Moreover, the vw mutation now adds a key mutation to the toolbox of understanding sensory perception. The uncovering of the norpA mutation can now help define the dynamics of phototransduction in Tribolium and permit an investigation in the role of vision in Tribolium behaviors, e.g. circadian rhythms. Overall due to the elimination of two other loci we propose that the vwmutation is now referred as Deficiency vermilionwhite , Df (vw).
","references":[{"reference":"
Adamski Z, Bufo SA, Chowański S, Falabella P, Lubawy J, Marciniak P, et al., Rosiński. 2019. Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies – A Review. Frontiers in Physiology 10: 10.3389/fphys.2019.00319.
","pubmedId":"","doi":"10.3389/fphys.2019.00319"},{"reference":"Adrianos S, Lorenzen M, Oppert B. 2018. Metabolic pathway interruption: CRISPR/Cas9-mediated knockout of tryptophan 2,3-dioxygenase in Tribolium castaneum. Journal of Insect Physiology 107: 104-109.
","pubmedId":"","doi":"10.1016/j.jinsphys.2018.03.004"},{"reference":"Berghammer AJ, Klingler M, A. Wimmer E. 1999. A universal marker for transgenic insects. Nature 402: 370-371.
","pubmedId":"","doi":"10.1038/46463"},{"reference":"Bloomquist BT, Shortridge RD, Schneuwly S, Perdew M, Montell C, Steller H, Rubin G, Pak WL. 1988. Isolation of a putative phospholipase c gene of drosophila, norpA, and its role in phototransduction. Cell 54: 723-733.
","pubmedId":"","doi":"10.1016/s0092-8674(88)80017-5"},{"reference":"Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, et al., Bateman. 2024. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Research 53: D444-D456.
","pubmedId":"","doi":"10.1093/nar/gkae1082"},{"reference":"Brown SJ, Shippy TD, Miller S, Bolognesi R, Beeman RW, Lorenzen MD, et al., Klingler. 2009. The Red Flour Beetle, Tribolium castaneum (Coleoptera): A Model for Studies of Development and Pest Biology: Figure 1.. Cold Spring Harbor Protocols 2009: pdb.emo126.
","pubmedId":"","doi":"10.1101/pdb.emo126"},{"reference":"Buetow L, Huang DT. 2016. Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nature Reviews Molecular Cell Biology 17: 626-642.
","pubmedId":"","doi":"10.1038/nrm.2016.91"},{"reference":"Campbell JF, Athanassiou CG, Hagstrum DW, Zhu KY. 2022. Tribolium castaneum: A Model Insect for Fundamental and Applied Research. Annual Review of Entomology 67: 347-365.
","pubmedId":"","doi":"10.1146/annurev-ento-080921-075157"},{"reference":"Cheng H, Asri M, Lucas J, Koren S, Li H. 2024. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nature Methods 21: 967-970.
","pubmedId":"","doi":"10.1038/s41592-024-02269-8"},{"reference":"Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18: 170-175.
","pubmedId":"","doi":"10.1038/s41592-020-01056-5"},{"reference":"Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, Li H. 2022. Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology 40: 1332-1335.
","pubmedId":"","doi":"10.1038/s41587-022-01261-x"},{"reference":"Childers AK, Geib SM, Sim SB, Poelchau MF, Coates BS, Simmonds TJ, et al., Scheffler. 2021. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects 12: 626.
","pubmedId":"","doi":"10.3390/insects12070626"},{"reference":"Corbalan-Garcia S, Gómez-Fernández JC. 2014. Signaling through C2 domains: More than one lipid target. Biochimica et Biophysica Acta (BBA) - Biomembranes 1838: 1536-1547.
","pubmedId":"","doi":"10.1016/j.bbamem.2014.01.008"},{"reference":"Croessmann S, Sheehan JH, Lee Km, Sliwoski G, He J, Nagy R, et al., Arteaga. 2018. PIK3CA\n C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3K\n α\n Inhibitors. Clinical Cancer Research 24: 1426-1435.
","pubmedId":"","doi":"10.1158/1078-0432.CCR-17-2141"},{"reference":"Davletov BA, Südhof TC. 1993. A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J Biol Chem 268(35): 26386-90.
","pubmedId":"8253763","doi":""},{"reference":"Eddleman, HL and Bell AE. 1963. Four new eye-color mutants in Tribolium castaneum (Abstr.). Genetics, 48, 888.
","pubmedId":"","doi":""},{"reference":"Haas MS, Beeman RW. 2012. Coming apart at the seams: morphological evidence for pregnathal head capsule borders in adult Tribolium castaneum. Development Genes and Evolution 222: 99-111.
","pubmedId":"","doi":"10.1007/s00427-012-0397-5"},{"reference":"Horn C, Jaunich B, Wimmer EA. 2000. Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Development Genes and Evolution 210: 623-629.
","pubmedId":"","doi":"10.1007/s004270000111"},{"reference":"Klingler M, Bucher G. 2022. The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. EvoDevo 13: 10.1186/s13227-022-00201-9.
","pubmedId":"","doi":"10.1186/s13227-022-00201-9"},{"reference":"Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094-3100.
","pubmedId":"","doi":"10.1093/bioinformatics/bty191"},{"reference":"Lorenzen MD, Brown SJ, Denell RE, Beeman RW. 2002. Transgene expression from the\n Tribolium castaneum Polyubiquitin\n promoter. Insect Molecular Biology 11: 399-407.
","pubmedId":"","doi":"10.1046/j.1365-2583.2002.00349.x"},{"reference":"Lorenzen MD, Brown SJ, Denell RE, Beeman RW. 2002. Cloning and Characterization of the Tribolium castaneum Eye-Color Genes Encoding Tryptophan Oxygenase and Kynurenine 3-Monooxygenase. Genetics 160: 225-234.
","pubmedId":"","doi":"10.1093/genetics/160.1.225"},{"reference":"Markley HC, Helms KJ, Maar M, Zentner GE, Wade MJ, Zelhof AC. 2024. Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. Journal of Insect Science 24: 10.1093/jisesa/ieae082.
","pubmedId":"","doi":"10.1093/jisesa/ieae082"},{"reference":"Pointer MD, Gage MJG, Spurgin LG. 2021. Tribolium beetles as a model system in evolution and ecology. Heredity 126: 869-883.
","pubmedId":"","doi":"10.1038/s41437-021-00420-1"},{"reference":"Rösner J, Wellmeyer B, Merzendorfer H. 2020. Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance. Current Pharmaceutical Design 26: 3554-3568.
","pubmedId":"","doi":"10.2174/1381612826666200513113140"},{"reference":"Tribolium Genome Sequencing Consortium. 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452: 949-955.
","pubmedId":"","doi":"10.1038/nature06784"}],"title":"Defining the breakpoints of the vermilion white (vw) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA.
","reviews":[],"curatorReviews":[]},{"id":"58d35af4-6da1-480b-b46b-ffe3bbe72c7a","decision":"publish","abstract":"A key mutation for generating transgenics in Tribolium castaneum is vermilionwhite (vw). vw is a deletion that removes most of the vermilion locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the Tribolium homolog of norpA. The vw deletion is 4434 bps. The deletion eliminates not only vermilion but also gustatory receptor candidate 58 and norpA function. Therefore, the vw mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency vermilionwhite, Df (vw).
","acknowledgements":"","authors":[{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["formalAnalysis","methodology","investigation","writing_originalDraft","writing_reviewEditing","dataCuration"],"email":"jojose@iu.edu","firstName":"Josy ","lastName":"Joseph","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0009-0006-2105-9580"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Center for Genomics and Bioinformatics"],"credit":["dataCuration","formalAnalysis","methodology","writing_reviewEditing"],"email":"drusch@iu.edu","firstName":"Douglas","lastName":"Rusch","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":"0000-0002-1066-2687"},{"affiliations":["Indiana University, Bloomington, IN, US"],"departments":["Biology"],"credit":["conceptualization","fundingAcquisition","investigation","supervision","writing_originalDraft","writing_reviewEditing"],"email":"azelhof@iu.edu","firstName":"Andrew","lastName":"Zelhof","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"000000017085822X"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[],"funding":"This work was supported by the National Science Foundation (IOS-1928781) to A.C.Z.
","image":{"url":"https://portal.micropublication.org/uploads/bf400e18706985db65b2d376b99e85e4.png"},"imageCaption":"A. Schematic of Tribolium castaneum genetic loci of three genes affected by vermilionwhite (vw) deletion. B. Coverage or depth of sequence alignment at genomic region specific to the vw deletion. Thirty nucleotides flanking each side of the 5′ and 3′ deletion breakpoints are highlighted, with red lines indicating the exact deletion boundaries. C. The amino acid sequence of exon 9 of norpA and the new open reading frame amino acids of exon 9 in vw. There is a stop codon after 15 amino acids. D. Comparison of protein structure of Phospholipase C between norpA and truncated norpA reveals the PH domain, Phosphoinositide phospholipase C beta1-4-like EF-hand domain and Phosphatidylinositol-specific phospholipase C domains remain intact but the C2 domain is truncated.
","imageTitle":"Genomic organization of the vw deletion
","methods":"Tribolium lines and husbandry: All animals were raised at 28oC on a standard flour yeast mix. The following strains were utilized: vermilionwhite (vw), and a strain heterozygous for vermilionwhite (vw) (Lorenzen et al., 2002a) and Lucifer (Lu) (Haas & Beeman, 2012).
Sequencing and genome assembly: 40 < 1 day old vermilionwhite (vw) and Lucifer (Lu) heterozygote pupae were isolated and immediately frozen in liquid nitrogen and stored at –80oC. Pupae were shipped on dry ice to Psomagen (https://www.psomagen.com/) for processing. DNA extraction, library construction, and PacBio sequencing were all performed by Psomagen. The PacBio hifi reads were assembled with hifiasm (v0.25.0-r726) (Cheng et al., 2024; Cheng et al., 2021; Cheng et al., 2022). The resulting assemblies as well as the input reads were mapped to the reference genome Tribolium castaneum strain icTriCast1.1 using minimap2 (v2.28) (Li, 2018) with default parameters. This identified a 4434 bp deletion. Among reads that span the deleted region, we identified 139 reads without the deletion and 149 reads that contain the deletion. The sequencing reads have been deposited in the SRA database and have the following accession numbers: SRR37271882 : wild-type vermilion locus reads and SRR37271883 : vw deletion locus reads.
norpA protein structure: The protein domains were compiled using InterPro (Blum et al., 2025).
","reagents":"","patternDescription":"Tribolium is a widely utilized model organism for evolutionary and developmental biology questions and understanding regulatory mechanisms for agricultural pests (Adamski et al., 2019; Brown et al., 2009; Pointer et al., 2021; Rosner et al., 2020). Tribolium was the first Coleoptera genome to be sequenced (Tribolium Genome Sequencing Consortium, 2008), and an updated genome sequence based upon long read sequencing (icTriCast1.1 - (Childers et al., 2021) is now available. Tribolium is amenable to both forward and reverse genetics, and in particular transgenesis is well established (Campbell et al., 2022; Klingler & Bucher, 2022). For transgenics, the 3XP3 fluorescent marked transposable elements is an efficient marker (Berghammer et al., 1999; Horn et al., 2000) and easily detected in Tribolium mutant retinas that lack pigmentation, e.g. pearl, platinum and white. Lorenzen et al. demonstrated that the Tribolium white mutation (Eddleman & Bell, 1963) is a null mutation of the Tribolium homolog of vermilion (Lorenzen et al., 2002a). Moreover, given the absence of pigment in vermilion mutant retinas, a set of transposable elements have been generated that result in the expression of vermilion and thus restores pigmentation to the retina (Lorenzen et al., 2002b). As a result, many Tribolium transgenics are generated in the vw mutant background.
The initial characterization of vermilionwhite demonstrated that the mutant is a deletion that removes the first five exons and extends into the last sixth exon of vermilion (Figure 1A). The upstream breakpoint was not mapped. To map the upstream breakpoint, we took advantage of PacBio long read sequence that contained the vw mutation. Our sequencing revealed a 4,434 bp deletion. The sequence confirmed the break point that lies within vermilion and identified the upstream second breakpoint (Figure 1B). The deletion eliminates the entire gustatory receptor candidate 58 locus and extends into the Tribolium norpA locus. norpA encodes a Phospholipase C which is critical for phototransduction and in its absence vision is disrupted (Bloomquist et al., 1988). The deletion results in a 3’ prime deletion of exon 9 of the norpA locus resulting in the truncation of the C2 domain of the phospholipase and an addition of 15 unrelated amino acids Figure 1C,D). The C2 domain is 91 amino-acid residues and thought to be involved in calcium-dependent phospholipid binding and membrane targeting (Davletov & Sudhof, 1993). The loss of the C2 domain can have multiple effects. It can prevent the protein from binding to the lipid bilayers (Croessmann et al., 2018) or it can impair the protein’s ability to respond to the calcium signals (Corbalan-Garcia & Gomez-Fernandez, 2014). The truncation can also reduce the stability of the protein, leading to premature degradation (Buetow & Huang, 2016). Thus the truncation of the C2 domain would suggest that the mutated norpA allele in the vw mutation is a loss of function allele.
With respect to the generation of transgenics, one will need to account for the additional mutations in vw but this concern can be alleviated using CRISPR/Cas9 generated vermilion alleles (Adrianos et al., 2018; Markley et al., 2024). Whereas the existence of two additional mutations may decrease the usefulness of vw with respect to transgenics, the existence of defined deletions has been critical for mapping of genes and confirming the nature of alleles. Moreover, the vw mutation now adds a key mutation to the toolbox of understanding sensory perception. The uncovering of the norpA mutation can now help define the dynamics of phototransduction in Tribolium and permit an investigation in the role of vision in Tribolium behaviors, e.g. circadian rhythms. Overall due to the elimination of two other loci we propose that the vwmutation is now referred as Deficiency vermilionwhite , Df (vw).
","references":[{"reference":"
Adamski Z, Bufo SA, Chowański S, Falabella P, Lubawy J, Marciniak P, et al., Rosiński. 2019. Beetles as Model Organisms in Physiological, Biomedical and Environmental Studies – A Review. Frontiers in Physiology 10: 10.3389/fphys.2019.00319.
","pubmedId":"","doi":"10.3389/fphys.2019.00319"},{"reference":"Adrianos S, Lorenzen M, Oppert B. 2018. Metabolic pathway interruption: CRISPR/Cas9-mediated knockout of tryptophan 2,3-dioxygenase in Tribolium castaneum. Journal of Insect Physiology 107: 104-109.
","pubmedId":"","doi":"10.1016/j.jinsphys.2018.03.004"},{"reference":"Berghammer AJ, Klingler M, A. Wimmer E. 1999. A universal marker for transgenic insects. Nature 402: 370-371.
","pubmedId":"","doi":"10.1038/46463"},{"reference":"Bloomquist BT, Shortridge RD, Schneuwly S, Perdew M, Montell C, Steller H, Rubin G, Pak WL. 1988. Isolation of a putative phospholipase c gene of drosophila, norpA, and its role in phototransduction. Cell 54: 723-733.
","pubmedId":"","doi":"10.1016/s0092-8674(88)80017-5"},{"reference":"Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, et al., Bateman. 2024. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Research 53: D444-D456.
","pubmedId":"","doi":"10.1093/nar/gkae1082"},{"reference":"Brown SJ, Shippy TD, Miller S, Bolognesi R, Beeman RW, Lorenzen MD, et al., Klingler. 2009. The Red Flour Beetle, Tribolium castaneum (Coleoptera): A Model for Studies of Development and Pest Biology: Figure 1.. Cold Spring Harbor Protocols 2009: pdb.emo126.
","pubmedId":"","doi":"10.1101/pdb.emo126"},{"reference":"Buetow L, Huang DT. 2016. Structural insights into the catalysis and regulation of E3 ubiquitin ligases. Nature Reviews Molecular Cell Biology 17: 626-642.
","pubmedId":"","doi":"10.1038/nrm.2016.91"},{"reference":"Campbell JF, Athanassiou CG, Hagstrum DW, Zhu KY. 2022. Tribolium castaneum: A Model Insect for Fundamental and Applied Research. Annual Review of Entomology 67: 347-365.
","pubmedId":"","doi":"10.1146/annurev-ento-080921-075157"},{"reference":"Cheng H, Asri M, Lucas J, Koren S, Li H. 2024. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nature Methods 21: 967-970.
","pubmedId":"","doi":"10.1038/s41592-024-02269-8"},{"reference":"Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18: 170-175.
","pubmedId":"","doi":"10.1038/s41592-020-01056-5"},{"reference":"Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, Li H. 2022. Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology 40: 1332-1335.
","pubmedId":"","doi":"10.1038/s41587-022-01261-x"},{"reference":"Childers AK, Geib SM, Sim SB, Poelchau MF, Coates BS, Simmonds TJ, et al., Scheffler. 2021. The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. Insects 12: 626.
","pubmedId":"","doi":"10.3390/insects12070626"},{"reference":"Corbalan-Garcia S, Gómez-Fernández JC. 2014. Signaling through C2 domains: More than one lipid target. Biochimica et Biophysica Acta (BBA) - Biomembranes 1838: 1536-1547.
","pubmedId":"","doi":"10.1016/j.bbamem.2014.01.008"},{"reference":"Croessmann S, Sheehan JH, Lee Km, Sliwoski G, He J, Nagy R, et al., Arteaga. 2018. PIK3CA\n C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3K\n α\n Inhibitors. Clinical Cancer Research 24: 1426-1435.
","pubmedId":"","doi":"10.1158/1078-0432.CCR-17-2141"},{"reference":"Davletov BA, Südhof TC. 1993. A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J Biol Chem 268(35): 26386-90.
","pubmedId":"8253763","doi":""},{"reference":"Eddleman, HL and Bell AE. 1963. Four new eye-color mutants in Tribolium castaneum (Abstr.). Genetics, 48, 888.
","pubmedId":"","doi":""},{"reference":"Haas MS, Beeman RW. 2012. Coming apart at the seams: morphological evidence for pregnathal head capsule borders in adult Tribolium castaneum. Development Genes and Evolution 222: 99-111.
","pubmedId":"","doi":"10.1007/s00427-012-0397-5"},{"reference":"Horn C, Jaunich B, Wimmer EA. 2000. Highly sensitive, fluorescent transformation marker for Drosophila transgenesis. Development Genes and Evolution 210: 623-629.
","pubmedId":"","doi":"10.1007/s004270000111"},{"reference":"Klingler M, Bucher G. 2022. The red flour beetle T. castaneum: elaborate genetic toolkit and unbiased large scale RNAi screening to study insect biology and evolution. EvoDevo 13: 10.1186/s13227-022-00201-9.
","pubmedId":"","doi":"10.1186/s13227-022-00201-9"},{"reference":"Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34: 3094-3100.
","pubmedId":"","doi":"10.1093/bioinformatics/bty191"},{"reference":"Lorenzen MD, Brown SJ, Denell RE, Beeman RW. 2002a. Cloning and Characterization of the Tribolium castaneum Eye-Color Genes Encoding Tryptophan Oxygenase and Kynurenine 3-Monooxygenase. Genetics 160: 225-234.
","pubmedId":"","doi":"10.1093/genetics/160.1.225"},{"reference":"Lorenzen MD, Brown SJ, Denell RE, Beeman RW. 2002b. Transgene expression from the Tribolium castaneum Polyubiquitin promoter. Insect Molecular Biology 11: 399-407.
","pubmedId":"","doi":"10.1046/j.1365-2583.2002.00349.x"},{"reference":"Markley HC, Helms KJ, Maar M, Zentner GE, Wade MJ, Zelhof AC. 2024. Generating and testing the efficacy of reagents for CRISPR/Cas9 homology directed repair-based manipulations in Tribolium. Journal of Insect Science 24: 10.1093/jisesa/ieae082.
","pubmedId":"","doi":"10.1093/jisesa/ieae082"},{"reference":"Pointer MD, Gage MJG, Spurgin LG. 2021. Tribolium beetles as a model system in evolution and ecology. Heredity 126: 869-883.
","pubmedId":"","doi":"10.1038/s41437-021-00420-1"},{"reference":"Rösner J, Wellmeyer B, Merzendorfer H. 2020. Tribolium castaneum: A Model for Investigating the Mode of Action of Insecticides and Mechanisms of Resistance. Current Pharmaceutical Design 26: 3554-3568.
","pubmedId":"","doi":"10.2174/1381612826666200513113140"},{"reference":"Tribolium Genome Sequencing Consortium. 2008. The genome of the model beetle and pest Tribolium castaneum. Nature 452: 949-955.
","pubmedId":"","doi":"10.1038/nature06784"}],"title":"Defining the breakpoints of the vermilion white (vw) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA.
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