Developing a gene model for the Peptidoglycan recognition protein SB1 ortholog (PGRP-SB1) in the ASM1890182v1 Genome Assembly (GenBank Accession: GCA_018901825.1) of Drosophila funebris. This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans-tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the Genomics Education Partnership. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. FlyBase is supported by grants: NHGRI U41HG000739 and U24HG010859, UK Medical Research Council MR/W024233/1, NSF 2035515 and 2039324, BBSRC BB/T014008/1, and Wellcome Trust PLM13398.
","authors":[{"affiliations":["App State, Boone, NC, US"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_reviewEditing","dataCuration"],"email":"mollymcdonaald@gmail.com","firstName":"Molly","lastName":"McDonald","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0009-9559-3825"},{"affiliations":["App State, Boone, NC, US"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_reviewEditing","validation"],"email":"chialvop@appstate.edu","firstName":"Pablo","lastName":"Chialvo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-3150-3167"},{"affiliations":["App State, Boone, NC, US"],"departments":["Biology"],"credit":["conceptualization","supervision","validation","writing_originalDraft"],"email":"chialvoch@appstate.edu","firstName":"Clare","lastName":"Scott Chialvo","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9029-3593"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[{"description":"Zipped archive containing FASTA, PEP, and GFF
","doi":null,"resourceType":"Dataset","name":"Dfun_PGRP-SB1_Model.tar.gz","url":"https://portal.micropublication.org/uploads/27c75a356476fe1293acfcf00dfeee09.gz"}],"funding":"This gene annotation project was funded by Nation Science Foundation grants DEB-1737869 (PI LKR, CoPI CSC) and DBI-2217912 (PI CSC). The Genomics Education Partnership (GEP; https://thegep.org/), which supports this project, is funded by the National Science Foundation (1915544; PI LKR) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517; PI LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.
","image":{"url":"https://portal.micropublication.org/uploads/a8e4e3f22fcf13fa78997e0a68944a1e.jpg"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for PGRP-SB1 in Drosophila melanogaster and Drosophila funebris. Thin underlying arrows indicate which DNA strand the target gene–PGRP-SB1–is located on in D. melanogaster (top) and D. funebris (bottom). The thin arrows pointing to the left indicate that PGRP-SB1 is on the negative strand in both D. melanogaster and D. funebris. The wide gene arrows pointing in the same direction as PGRP-SB1 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of PGRP-SB1 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. funebris indicate orthology to the corresponding gene in D. melanogaster, while black gene arrows indicate non-orthology and grey gene arrows indicate that the gene is present in both neighborhoods but not syntenic. Gene symbols given in the D. funebris gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. funebris. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of PGRP-SB1 in D. funebris are displayed in the User Supplied Track (red); coding sequences (CDS) are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Coding Regions Predicted by Augustus (dark blue), GeMoMa (teal), and NSCAN PASA-EST (dark green), and RNA-Seq from mixed sex adult flies (brown; alignment of Illumina RNA-Seq reads from D. funebris – Erlenbach et al., 2023). (C) Dot Plot of PGRP-SB1-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. funebris (y-axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. Line breaks in the dot plot indicate areas of with low sequence identity between species. One longer break is present that extends across all of CDS 1 and the beginning of CDS 2 (dark purple box – a). A smaller break is also present towards the end of CDS 2 (yellow box – b). (D) Idiosyncrasies in protein alignment. The protein model contains one longer break and a shorter break that indicate areas of low sequence identity. In the longer break that extends across all of CDS 1 and into CDS 2 (dark purple box – a), only two of the 25 amino acids are highly dissimilar. There is one fewer amino acid in CDS 1 of D. funebris, and an insertion of three amino acids is present at the beginning of CDS 2 of D. funebris. The shorter break that occurs towards the end of CDS 2 (yellow box – b) spans a region of 11 amino acids only one of which is highly dissimilar.
","imageTitle":"Genomic neighborhood and gene model for PGRP-SB1 in D. funebris
","methods":"The annotation methods used in this project are adapted from those described in Rele et al. (2023), which includes algorithms, database versions, and citations for the complete annotation process developed for the Pathways Project. The methods for the current project are detailed in brief below with notes on significant differences between this protocol and the one described in Rele et al. (2023). The students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent et al., 2002; Raney et al., 2024) to examine the genomic neighborhood of their reference detoxification gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students obtain the protein sequence for the D. melanogaster target gene for a given isoform and use a tblastn search of the sequence against their target Drosophila species genome assembly (D. funebris (GCA_018901825.1 – Kim et al., 2013)) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify the putative ortholog location. Students compare the genomic neighborhood of the putative ortholog to that of the reference gene in D. melanogaster. This local synteny analysis includes a minimum of two upstream and downstream genes relative to the potential ortholog. As no RefSeq protein data is available for these species, comparisons are based on gene predictions that correlate with gene expression data in the putative ortholog neighborhood. Using the multiple alignment tracks feature in the Genome Browser, students examine other sets of genomic evidence, including Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Augustus, NSCAN PASA-EST), and mixed sex RNA-Seq adult expression data from the target species generated by Erlenbach et al. (2023; https://doi.org/10.5061/dryad.hdr7sqvq2). Information on the genomic structure information (e.g., CDSs, intron-exon number, number of isoforms) for the reference gene in D. melanogaster is retrieved using Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). To determine approximate splice sites within the target gene, a tblastn search using the CDSs from the D. melanogaster reference gene against the putative ortholog location (10kb up- and downstream of the target gene prediction). Coordinates of the CDS(s) are refined by examining aligned RNA-Seq data, identifying canonical splice site sequences, and ensuring the maintenance of an open reading frame. Students confirm the biological validity of their target gene model using the FlySeq Gene Model Checker (https://gander2.wustl.edu/~wilson/genechecker-flyseq/), which compares the hypothesized target gene model’s structure and translated sequence against the D. melanogaster reference gene. At least two independent models for this gene are generated. These models are reconciled by a third independent researcher to produce the final model presented here. Note: comparison of 5' and 3' UTR sequence information is not included in this GEP CURE protocol.
","reagents":"","patternDescription":"Introduction
This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org) for Course-based Undergraduate Research Experience (CURE). The following information in this box may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster detoxification genes.
“Within insects, the process of detoxifying xenobiotics and host secondary metabolites is a three-phase process that involves functionalization, conjugation, and excretion of these compounds. Expansions of known detoxification gene families (e.g., cytochrome P450s) is associated with diet breadth and insecticide resistance (Ranson et al., 2002; Després et al., 2007; Rane et al., 2016). With the increasing availability of high-quality genomes for non-model organisms, including Drosophila species beyond D. melanogaster, it is now possible to perform large scale comparative studies (Robinson et al., 2011; Kim et al., 2021; Threfall and Baxter, 2021). Careful manual annotation and curation of gene models can improve upon computational gene predictions in non-model species, which aids the accuracy of studies on gene and genome evolution (Mudge and Harrow, 2016; Tello-Ruiz et al., 2019). To aid in these annotations, the Genomics Education Partnership (thegep.org) developed a curriculum involving web-based tools that allow undergraduates to engage in authentic course-based research focused on manually annotating genes in non-model species (Rele et al., 2023). The orthologous gene models, including the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The gene ortholog described here in D. funebris for Peptidoglycan recognition protein SB1 (PGRP-SB1), a member of the peptidoglycan recognition protein that contributes to the innate immune system of insects, was characterized as part of a developing dataset for a comparative study of detoxification gene families in the immigrans-tripunctata radiation of the genus Drosophila.” (Williams et al., 2026)
The type species of the genus Drosophila, D. funebris (Fabricius, 1787), is a member of the funebris species group, which occurs in the immigrans-tripunctata radiation of the Drosophila subgenus (Bächli, 2005; ICZN, 2010). This species is a globally distributed human commensal (Grimaldi, 2022). While D. funebris feeds on shelf fungi and fruit (Kimura et al., 1977; Prigent et al., 2003), it does not tolerate the mushroom toxin α-amanitin (Stump et al., 2011; Erlenbach et al., 2023).
When considering the detoxification of xenobiotics, the focus is often directed towards genes that produce detoxification enzymes. A growing body of work is beginning to highlight the role of genes in the insect’s innate immune system in metabolizing these toxic compounds (Bartling et al., 2021; Jiang et al., 2021; Rahmat et al., 2024). One component of the innate immune system, peptidoglycan recognition proteins (PGRP), are pattern recognition molecules that detect molecular patterns found in pathogens but absent in the host organism (Akira et al., 2006; Lemaitre and Hoffman, 2007). Within Drosophila melanogaster, Werner et al. (2000) identified 12 PGRPs. These proteins are split into two subgroups (long and short) based on their transcript size, cellular location, and function (Werner et al., 2000). Peptidoglycan recognition protein SB1 (PGRP-SB1) is a short PGRP (Werner et al., 2000). It is an amidase that exhibits antibacterial activity against peptidoglycans that possess a diaminopimelic acid residue (Mellroth and Steiner, 2006). When Drosophila flies are exposed to wasp, mite, or nematode parasites, the expression of this gene is increased (Benoit et al., 2020). In addition, exposure to sublethal doses of six insecticides also increased the expression of PGRP-SB1 (Gao et al., 2021).
We propose a gene model for the D. funebris ortholog of the D. melanogaster Peptidoglycan recognition protein SB1 (PGRP-SB1) gene. The genomic region of the ortholog corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 in the ASM1890182v1 Genome Assembly of D. funebris (GCA_018901825.1- Kim et al. 2021). This model is based on mixed sex, adult RNA-Seq data from D. funebris (Erlenbach et al. 2023; https://doi.org/10.5061/dryad.hdr7sqvq2) and PGRP-SB1 in D. melanogaster using FlyBase release FB2024_02 (GCA_000001215.4; Gramates et al., 2022; Jenkins et al., 2022; Larkin et al., 2021).
Synteny
The reference gene, PGRP-SB1, occurs on chromosome 3L in D. melanogaster and is flanked upstream by Dead box protein 73D (Dbp73D) and CG9701 and downstream by Peptidoglycan recognition protein SB2 (PGRP-SB2) and CG13026. The tblastn search of D. melanogaster PGRP-SB1-PA (query) against the D. funebris (GenBank Accession: GCA_018901825.1 Genome Assembly database (subject) placed the putative ortholog of PGRP-SB1 within contig_693 (JAEIFK010000688) which corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 (E-value: 3.00e-113; percent identity: 78.2%; query coverage: 98% as determined by blastp). The putative ortholog is flanked upstream by Augustus gene predictions JAEIFK010000688.g513.t1 and JAEIFK010000688.g514.t1, which correspond to Dbp73D and CG9701 in D. melanogaster (E-value: 0.0 and 0.0; identity: 66.47% and 88.70%, respectively, as determined by blastp; Figure 1A; Altschul et al., 1990). The putative ortholog of PGRP-SB1 is flanked downstream by JAEIFK010000688.g511.t1 and JAEIFK010000688.g510.t1, which correspond to CG13026 and Disabled (Dab) in D. melanogaster (E-value: 1.00e-13 and 0.0 identity: 52.75% and 68.16%, respectively, as determined by blastp). Dab is the third gene downstream of the target gene, PGRP-SB1, in D. melanogaster. The putative ortholog assignment for PGRP-SB1 in D. funebris is supported by the following evidence: The gene predictions surrounding the PGRP-SB1 ortholog are all orthologous to the genes at the same locus in D. melanogaster except for the loss of the PGRP-SB2 gene, gene expression data corresponds with each prediction, and local synteny is almost entirely conserved, supported by E-values and percent identities, so we conclude that JAEIFK010000688.g512.t1 is an ortholog of PGRP-SB1 in D. funebris (Figure 1A).
Protein Model
PGRP-SB1 in D. funebris has 2 coding sequences (CDS) within the genome sequence. The only unique protein sequence (PGRP-SB1-PA) is translated from 1 mRNA isoform (PGRP-SB1-RA; Figure 1B). Relative to the ortholog in D. melanogaster, the CDS number and protein isoform count are conserved. The sequence of PGRP-SB1-PA in D. funebris has 78.1% identity (89.1% similarity) with the protein-coding isoform PGRP-SB1-PA in D. melanogaster, as determined by blastp (Figure 1C). This level of divergence is not surprising given that D. funebris and D. melanogaster belong to two separate subgenera (Drosophila and Sophophora respectively) that diverged approximately 45-60MYA (Russo et al., 1995; Tamura et al., 2004; Obbard et al., 2012). Coordinates of this curated gene model are archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"reference":"Akira S, Uematsu S, Takeuchi O. 2006. Pathogen recognition and innate immunity. Cell 124(4): 783-801.
","pubmedId":"16497588","doi":""},{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.
","pubmedId":"2231712","doi":""},{"reference":"Bächli, G. (2005) Taxodros: The database on taxonomy of Drosophilidae, version February 2026, last accessed 28 May 2026. https://taxodros.uzh.ch/
","pubmedId":"","doi":""},{"reference":"Bartling MT, Thümecke S, Russert JH, Vilcinskas A, Lee KZ. 2021. Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees. Sci Rep 11(1): 6819.
","pubmedId":"33767272","doi":""},{"reference":"Benoit JB, Bose J, Bailey ST, Polak M. 2020. Interactions with ectoparasitic mites induce host metabolic and immune responses in flies at the expense of reproduction-associated factors. Parasitology 147(11): 1196-1205.
","pubmedId":"32498733","doi":""},{"reference":"Després L, David JP, Gallet C. 2007. The evolutionary ecology of insect resistance to plant chemicals. Trends Ecol Evol 22(6): 298-307.
","pubmedId":"17324485","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.
","pubmedId":"17994087","doi":""},{"reference":"Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone SA, Reed LK, Dyer KA, Scott Chialvo CH. 2023. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 13(12): e10736.
","pubmedId":"38099137","doi":""},{"reference":"Fabricius JC, Metcalf Collection (North Carolina State University)., Tippmann Collection (North Carolina State University).. 1787. Mantissa insectorum sistens eorum species nuper detectas adiectis characteribus genericis, differentiis specificis, emendationibus, observationibus, Ioh. Christ. Fabricii.. : 10.5962/bhl.title.36471.
","pubmedId":"","doi":"10.5962/bhl.title.36471"},{"reference":"Gao Y, Kim JH, Jeong IH, Clark JM, Lee SH. 2021. Transcriptomic identification and characterization of genes commonly responding to sublethal concentrations of six different insecticides in the common fruit fly, Drosophila melanogaster. Pestic Biochem Physiol 175: 104852.
","pubmedId":"33993970","doi":""},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al., the FlyBase Consortium. 2022. FlyBase: a guided tour of highlighted features. Genetics 220(4): 10.1093/genetics/iyac035.
","pubmedId":"35266522","doi":""},{"reference":"Grimaldi DA. 2022. The Drosophila funebris Species Group in North America (Diptera: Drosophilidae). American Museum Novitates 2022: 10.1206/3988.1.
","pubmedId":"","doi":"10.1206/3988.1"},{"reference":"ICZN. (2010) Opinion 2245 (Case 3407): Drosophila Fallén, 1823 (Insecta, Diptera): Drosophila funebris Fabricius, 1787 is maintained as the type species. The Bulletin of Zoological Nomenclature 67(1), 106-115.
","pubmedId":"","doi":"10.21805/bzn.v67i1.a14"},{"reference":"Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.
","pubmedId":"35980571","doi":""},{"reference":"Jiang DL, Ding JH, Liu ZX, Shao ZM, Liang XH, Wang J, Wu FA, Sheng S. 2021. A role of peptidoglycan recognition protein in mediating insecticide detoxification in Glyphodes pyloalis. Arch Insect Biochem Physiol 108(3): e21842.
","pubmedId":"34499777","doi":""},{"reference":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6): 996-1006.
","pubmedId":"12045153","doi":""},{"reference":"Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, et al., Petrov DA. 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife 10: 10.7554/eLife.66405.
","pubmedId":"34279216","doi":""},{"reference":"Kimura M, Toda M, Beppu K, Watabe H. (1977) Breeding sites of Drosophilid flies in and near Sapporo northern Japan, with supplementary notes on adult feeding habits. Japanese Journal of Entomology 45: 571-582.
","pubmedId":"","doi":""},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.
","pubmedId":"33219682","doi":""},{"reference":"Lemaitre B, Hoffmann J. 2007. The host defense of Drosophila melanogaster. Annu Rev Immunol 25: 697-743.
","pubmedId":"17201680","doi":""},{"reference":"Mellroth P, Steiner H. 2006. PGRP-SB1: an N-acetylmuramoyl L-alanine amidase with antibacterial activity. Biochem Biophys Res Commun 350(4): 994-9.
","pubmedId":"17046713","doi":""},{"reference":"Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.
","pubmedId":"27773922","doi":""},{"reference":"Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM. 2012. Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol 29(11): 3459-73.
","pubmedId":"22683811","doi":""},{"reference":"Prigent Sp, Renard E, Cariou ML. 2003. Electrophoretic Mobility of Amylase in Drosophilids Indicates Adaptation to Ecological Diversity. Genetica 119: 133-145.
","pubmedId":"","doi":"10.1023/A:1026071317995"},{"reference":"Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. 2024. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 112: 108176.
","pubmedId":"39181100","doi":""},{"reference":"Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S, Oakeshott JG. 2016. Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Curr Opin Insect Sci 13: 70-76.
","pubmedId":"27436555","doi":""},{"reference":"Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, et al., Haeussler M. 2024. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res 52(D1): D1082-D1088.
","pubmedId":"37953330","doi":""},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.
","pubmedId":"24227676","doi":""},{"reference":"Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova MV, et al., Feyereisen R. 2002. Evolution of supergene families associated with insecticide resistance. Science 298(5591): 179-81.
","pubmedId":"12364796","doi":""},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Res 11: 1579.
","pubmedId":"37854289","doi":""},{"reference":"Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, et al., Schneider DJ. 2011. Creating a buzz about insect genomes. Science 331(6023): 1386.
","pubmedId":"21415334","doi":""},{"reference":"Russo CA, Takezaki N, Nei M. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12(3): 391-404.
","pubmedId":"7739381","doi":""},{"reference":"Stump AD, Jablonski SE, Bouton L, Wilder JA. 2011. Distribution and mechanism of α-amanitin tolerance in mycophagous Drosophila (Diptera: Drosophilidae). Environ Entomol 40(6): 1604-12.
","pubmedId":"22217779","doi":""},{"reference":"Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21(1): 36-44.
","pubmedId":"12949132","doi":""},{"reference":"Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, et al., Micklos DA. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One 14(10): e0224086.
","pubmedId":"31658277","doi":""},{"reference":"Threlfall J, Blaxter M. 2021. Launching the Tree of Life Gateway. Wellcome Open Res 6: 125.
","pubmedId":"34095514","doi":""},{"reference":"Werner T, Liu G, Kang D, Ekengren S, Steiner H, Hultmark D. 2000. A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster. Proc Natl Acad Sci U S A 97(25): 13772-7.
","pubmedId":"11106397","doi":""},{"reference":"Williams E, Chialvo P, Scott Chialvo C. 2026. Gene model for the ortholog of GstO3 in Drosophila dunni. microPublication Biology. 10.17912/micropub.biology.002110.
","pubmedId":"","doi":""}],"title":"Gene model for the ortholog of PGRP-SB1 in Drosophila funebris
","reviews":[{"reviewer":{"displayName":"Amie Jo McClellan"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"24ee686f-f51f-4381-b118-5941fceda186","decision":"edit","abstract":"We developed a gene model for the Peptidoglycan recognition protein SB1 ortholog (PGRP-SB1) in the ASM1890182v1 Genome Assembly (GenBank Accession: GCA_018901825.1) of Drosophila funebris. This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans-tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the Genomics Education Partnership. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. FlyBase is supported by grants: NHGRI U41HG000739 and U24HG010859, UK Medical Research Council MR/W024233/1, NSF 2035515 and 2039324, BBSRC BB/T014008/1, and Wellcome Trust PLM13398.
","authors":[{"affiliations":["App State, Boone, NC, United States"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_reviewEditing","dataCuration"],"email":"mollymcdonaald@gmail.com","firstName":"Molly","lastName":"McDonald","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0009-9559-3825"},{"affiliations":["App State, Boone, NC, United States"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_reviewEditing","validation"],"email":"chialvop@appstate.edu","firstName":"Pablo","lastName":"Chialvo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-3150-3167"},{"affiliations":["App State, Boone, NC, United States"],"departments":["Biology"],"credit":["conceptualization","supervision","validation","writing_originalDraft"],"email":"chialvoch@appstate.edu","firstName":"Clare","lastName":"Scott Chialvo","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9029-3593"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[{"description":"Zipped archive containing FASTA, PEP, and GFF
","doi":null,"resourceType":"Dataset","name":"Dfun_PGRP-SB1_Model.tar.gz","url":"https://portal.micropublication.org/uploads/27c75a356476fe1293acfcf00dfeee09.gz"}],"funding":"This gene annotation project was funded by Nation Science Foundation grants DEB-1737869 (PI LKR, CoPI CSC) and DBI-2217912 (PI CSC). The Genomics Education Partnership (GEP; https://thegep.org/), which supports this project, is funded by the National Science Foundation (1915544; PI LKR) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517; PI LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.
","image":{"url":"https://portal.micropublication.org/uploads/a8e4e3f22fcf13fa78997e0a68944a1e.jpg"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for PGRP-SB1 in Drosophila melanogaster and Drosophila funebris. Thin underlying arrows indicate which DNA strand the target gene–PGRP-SB1–is located on in D. melanogaster (top) and D. funebris (bottom). The thin arrows pointing to the left indicate that PGRP-SB1 is on the negative strand in both D. melanogaster and D. funebris. The wide gene arrows pointing in the same direction as PGRP-SB1 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of PGRP-SB1 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. funebris indicate orthology to the corresponding gene in D. melanogaster, while black gene arrows indicate non-orthology and grey gene arrows indicate that the gene is present in both neighborhoods but not syntenic. Gene symbols given in the D. funebris gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. funebris. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of PGRP-SB1 in D. funebris are displayed in the User Supplied Track (red); coding sequences (CDS) are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Coding Regions Predicted by Augustus (dark blue), GeMoMa (teal), and NSCAN PASA-EST (dark green), and RNA-Seq from mixed sex adult flies (brown; alignment of Illumina RNA-Seq reads from D. funebris – Erlenbach et al., 2023). (C) Dot Plot of PGRP-SB1-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. funebris (y-axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. Line breaks in the dot plot indicate areas of with low sequence identity between species. One longer break is present that extends across all of CDS 1 and the beginning of CDS 2 (dark purple box – a). A smaller break is also present towards the end of CDS 2 (yellow box – b). (D) Idiosyncrasies in protein alignment. The protein model contains one longer break and a shorter break that indicate areas of low sequence identity. In the longer break that extends across all of CDS 1 and into CDS 2 (dark purple box – a), only two of the 25 amino acids are highly dissimilar. There is one fewer amino acid in CDS 1 of D. funebris, and an insertion of three amino acids is present at the beginning of CDS 2 of D. funebris. The shorter break that occurs towards the end of CDS 2 (yellow box – b) spans a region of 11 amino acids, only one of which is highly dissimilar.
","imageTitle":"Genomic neighborhood and gene model for PGRP-SB1 in D. funebris
","methods":"The annotation methods used in this project are adapted from those described in Rele et al. (2023), which includes algorithms, database versions, and citations for the complete annotation process developed for the Pathways Project. The methods for the current project are detailed in brief below with notes on significant differences between this protocol and the one described in Rele et al. (2023). The students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent et al., 2002; Raney et al., 2024) to examine the genomic neighborhood of their reference detoxification gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students obtain the protein sequence for the D. melanogaster target gene for a given isoform and use a tblastn search of the sequence against their target Drosophila species genome assembly (D. funebris (GCA_018901825.1 – Kim et al., 2013)) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify the putative ortholog location. Students compare the genomic neighborhood of the putative ortholog to that of the reference gene in D. melanogaster. This local synteny analysis includes a minimum of two upstream and downstream genes relative to the potential ortholog. As no RefSeq protein data is available for these species, comparisons are based on gene predictions that correlate with gene expression data in the putative ortholog neighborhood. Using the multiple alignment tracks feature in the Genome Browser, students examine other sets of genomic evidence, including Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Augustus, NSCAN PASA-EST), and mixed sex RNA-Seq adult expression data from the target species generated by Erlenbach et al. (2023; https://doi.org/10.5061/dryad.hdr7sqvq2). Information on the genomic structure information (e.g., CDSs, intron-exon number, number of isoforms) for the reference gene in D. melanogaster is retrieved using Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). To determine approximate splice sites within the target gene, a tblastn search using the CDSs from the D. melanogaster reference gene against the putative ortholog location (10kb up- and downstream of the target gene prediction). Coordinates of the CDS(s) are refined by examining aligned RNA-Seq data, identifying canonical splice site sequences, and ensuring the maintenance of an open reading frame. Students confirm the biological validity of their target gene model using the FlySeq Gene Model Checker (https://gander2.wustl.edu/~wilson/genechecker-flyseq/), which compares the hypothesized target gene model's structure and translated sequence against the D. melanogaster reference gene. At least two independent models for this gene are generated. These models are reconciled by a third independent researcher to produce the final model presented here. Note: comparison of 5' and 3' UTR sequence information is not included in this GEP CURE protocol.
","reagents":"","patternDescription":"Introduction
This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org) for Course-based Undergraduate Research Experience (CURE). The following information in quotes may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster detoxification genes.
“Within insects, the process of detoxifying xenobiotics and host secondary metabolites is a three-phase process that involves functionalization, conjugation, and excretion of these compounds. Expansions of known detoxification gene families (e.g., cytochrome P450s) is associated with diet breadth and insecticide resistance (Ranson et al., 2002; Després et al., 2007; Rane et al., 2016). With the increasing availability of high-quality genomes for non-model organisms, including Drosophila species beyond D. melanogaster, it is now possible to perform large scale comparative studies (Robinson et al., 2011; Kim et al., 2021; Threfall and Baxter, 2021). Careful manual annotation and curation of gene models can improve upon computational gene predictions in non-model species, which aids the accuracy of studies on gene and genome evolution (Mudge and Harrow, 2016; Tello-Ruiz et al., 2019). To aid in these annotations, the Genomics Education Partnership (thegep.org) developed a curriculum involving web-based tools that allow undergraduates to engage in authentic course-based research focused on manually annotating genes in non-model species (Rele et al., 2023). The orthologous gene models, including the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The gene ortholog described here in D. funebris for Peptidoglycan recognition protein SB1 (PGRP-SB1), a member of the peptidoglycan recognition protein family that contributes to the innate immune system of insects, was characterized as part of a developing dataset for a comparative study of detoxification gene families in the immigrans-tripunctata radiation of the genus Drosophila.” (Williams et al., 2026)
Drosophila funebris (Fabricius, 1787) is a member of the funebris species group, which occurs in the immigrans-tripunctata radiation of the Drosophila subgenus (Bächli, 2005; ICZN, 2010). It is also the type species of the genus Drosophila. This species is a globally distributed human commensal (Grimaldi, 2022). While D. funebris feeds on shelf fungi and fruit (Kimura et al., 1977; Prigent et al., 2003), it does not tolerate the mushroom toxin α-amanitin (Stump et al., 2011; Erlenbach et al., 2023).
When considering the detoxification of xenobiotics, the focus is often directed towards genes that produce detoxification enzymes. A growing body of work is beginning to highlight the role of genes in the insect's innate immune system in metabolizing these toxic compounds (Bartling et al., 2021; Jiang et al., 2021; Rahmat et al., 2024). One component of the innate immune system, peptidoglycan recognition proteins (PGRP), are pattern recognition molecules that detect molecular patterns found in pathogens but absent in the host organism (Akira et al., 2006; Lemaitre and Hoffman, 2007). Within Drosophila melanogaster, Werner et al. (2000) identified 12 PGRPs. These proteins are split into two subgroups (long and short) based on their transcript size, cellular location, and function (Werner et al., 2000). Peptidoglycan recognition protein SB1 (PGRP-SB1) is a short PGRP (Werner et al., 2000). It is an amidase that exhibits antibacterial activity against peptidoglycans that possess a diaminopimelic acid residue (Mellroth and Steiner, 2006). When Drosophila flies are exposed to wasp, mite, or nematode parasites, the expression of this gene is increased (Benoit et al., 2020). In addition, exposure to sublethal doses of six insecticides also increased the expression of PGRP-SB1 (Gao et al., 2021).
We propose a gene model for the D. funebris ortholog of the D. melanogaster Peptidoglycan recognition protein SB1 (PGRP-SB1) gene. The genomic region of the ortholog corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 in the ASM1890182v1 Genome Assembly of D. funebris (GCA_018901825.1- Kim et al. 2021). This model is based on mixed sex, adult RNA-Seq data from D. funebris (Erlenbach et al. 2023; https://doi.org/10.5061/dryad.hdr7sqvq2) and PGRP-SB1 in D. melanogaster using FlyBase release FB2024_02 (GCA_000001215.4; Gramates et al., 2022; Jenkins et al., 2022; Larkin et al., 2021).
Synteny
The reference gene, PGRP-SB1, occurs on chromosome 3L in D. melanogaster and is flanked upstream by Dead box protein 73D (Dbp73D) and CG9701 and downstream by Peptidoglycan recognition protein SB2 (PGRP-SB2) and CG13026. The tblastn search of D. melanogaster PGRP-SB1-PA (query) against the D. funebris (GenBank Accession: GCA_018901825.1 Genome Assembly database (subject) placed the putative ortholog of PGRP-SB1 within contig_693 (JAEIFK010000688) which corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 (E-value: 3.00e-113; percent identity: 78.2%; query coverage: 98% as determined by blastp). The putative ortholog is flanked upstream by Augustus gene predictions JAEIFK010000688.g513.t1 and JAEIFK010000688.g514.t1, which correspond to Dbp73D and CG9701 in D. melanogaster (E-value: 0.0 and 0.0; identity: 66.47% and 88.70%, respectively, as determined by blastp; Figure 1A; Altschul et al., 1990). The putative ortholog of PGRP-SB1 is flanked downstream by JAEIFK010000688.g511.t1 and JAEIFK010000688.g510.t1, which correspond to CG13026 and Disabled (Dab) in D. melanogaster (E-value: 1.00e-13 and 0.0 identity: 52.75% and 68.16%, respectively, as determined by blastp). Dab is the third gene downstream of the target gene, PGRP-SB1, in D. melanogaster. The putative ortholog assignment for PGRP-SB1 in D. funebris is supported by the following evidence: The gene predictions surrounding the PGRP-SB1 ortholog are all orthologous to the genes at the same locus in D. melanogaster except for the loss of the PGRP-SB2 gene, gene expression data corresponds with each prediction, and local synteny is almost entirely conserved, supported by E-values and percent identities, so we conclude that JAEIFK010000688.g512.t1 is an ortholog of PGRP-SB1 in D. funebris (Figure 1A).
Protein Model
PGRP-SB1 in D. funebris has 2 coding sequences (CDS) within the genome sequence. The only unique protein sequence (PGRP-SB1-PA) is translated from 1 mRNA isoform (PGRP-SB1-RA; Figure 1B). Relative to the ortholog in D. melanogaster, the CDS number and protein isoform count are conserved. The sequence of PGRP-SB1-PA in D. funebris has 78.1% identity (89.1% similarity) with the protein-coding isoform PGRP-SB1-PA in D. melanogaster, as determined by blastp (Figure 1C). This level of divergence is not surprising given that D. funebris and D. melanogaster belong to two separate subgenera (Drosophila and Sophophora respectively) that diverged approximately 45-60 MYA (Russo et al., 1995; Tamura et al., 2004; Obbard et al., 2012). Coordinates of this curated gene model are archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"reference":"Akira S, Uematsu S, Takeuchi O. 2006. Pathogen recognition and innate immunity. Cell 124(4): 783-801.
","pubmedId":"16497588","doi":""},{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.
","pubmedId":"2231712","doi":""},{"reference":"Bächli, G. (2005) Taxodros: The database on taxonomy of Drosophilidae, version February 2026, last accessed 28 May 2026. https://taxodros.uzh.ch/
","pubmedId":"","doi":""},{"reference":"Bartling MT, Thümecke S, Russert JH, Vilcinskas A, Lee KZ. 2021. Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees. Sci Rep 11(1): 6819.
","pubmedId":"33767272","doi":""},{"reference":"Benoit JB, Bose J, Bailey ST, Polak M. 2020. Interactions with ectoparasitic mites induce host metabolic and immune responses in flies at the expense of reproduction-associated factors. Parasitology 147(11): 1196-1205.
","pubmedId":"32498733","doi":""},{"reference":"Després L, David JP, Gallet C. 2007. The evolutionary ecology of insect resistance to plant chemicals. Trends Ecol Evol 22(6): 298-307.
","pubmedId":"17324485","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.
","pubmedId":"17994087","doi":""},{"reference":"Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone SA, Reed LK, Dyer KA, Scott Chialvo CH. 2023. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 13(12): e10736.
","pubmedId":"38099137","doi":""},{"reference":"Fabricius JC, Metcalf Collection (North Carolina State University)., Tippmann Collection (North Carolina State University).. 1787. Mantissa insectorum sistens eorum species nuper detectas adiectis characteribus genericis, differentiis specificis, emendationibus, observationibus, Ioh. Christ. Fabricii.. : 10.5962/bhl.title.36471.
","pubmedId":"","doi":"10.5962/bhl.title.36471"},{"reference":"Gao Y, Kim JH, Jeong IH, Clark JM, Lee SH. 2021. Transcriptomic identification and characterization of genes commonly responding to sublethal concentrations of six different insecticides in the common fruit fly, Drosophila melanogaster. Pestic Biochem Physiol 175: 104852.
","pubmedId":"33993970","doi":""},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al., the FlyBase Consortium. 2022. FlyBase: a guided tour of highlighted features. Genetics 220(4): 10.1093/genetics/iyac035.
","pubmedId":"35266522","doi":""},{"reference":"Grimaldi DA. 2022. The Drosophila funebris Species Group in North America (Diptera: Drosophilidae). American Museum Novitates 2022: 10.1206/3988.1.
","pubmedId":"","doi":"10.1206/3988.1"},{"reference":"ICZN. (2010) Opinion 2245 (Case 3407): Drosophila Fallén, 1823 (Insecta, Diptera): Drosophila funebris Fabricius, 1787 is maintained as the type species. The Bulletin of Zoological Nomenclature 67(1), 106-115.
","pubmedId":"","doi":"10.21805/bzn.v67i1.a14"},{"reference":"Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.
","pubmedId":"35980571","doi":""},{"reference":"Jiang DL, Ding JH, Liu ZX, Shao ZM, Liang XH, Wang J, Wu FA, Sheng S. 2021. A role of peptidoglycan recognition protein in mediating insecticide detoxification in Glyphodes pyloalis. Arch Insect Biochem Physiol 108(3): e21842.
","pubmedId":"34499777","doi":""},{"reference":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6): 996-1006.
","pubmedId":"12045153","doi":""},{"reference":"Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, et al., Petrov DA. 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife 10: 10.7554/eLife.66405.
","pubmedId":"34279216","doi":""},{"reference":"Kimura M, Toda M, Beppu K, Watabe H. (1977) Breeding sites of Drosophilid flies in and near Sapporo northern Japan, with supplementary notes on adult feeding habits. Japanese Journal of Entomology 45: 571-582.
","pubmedId":"","doi":""},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.
","pubmedId":"33219682","doi":""},{"reference":"Lemaitre B, Hoffmann J. 2007. The host defense of Drosophila melanogaster. Annu Rev Immunol 25: 697-743.
","pubmedId":"17201680","doi":""},{"reference":"Mellroth P, Steiner H. 2006. PGRP-SB1: an N-acetylmuramoyl L-alanine amidase with antibacterial activity. Biochem Biophys Res Commun 350(4): 994-9.
","pubmedId":"17046713","doi":""},{"reference":"Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.
","pubmedId":"27773922","doi":""},{"reference":"Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM. 2012. Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol 29(11): 3459-73.
","pubmedId":"22683811","doi":""},{"reference":"Prigent Sp, Renard E, Cariou ML. 2003. Electrophoretic Mobility of Amylase in Drosophilids Indicates Adaptation to Ecological Diversity. Genetica 119: 133-145.
","pubmedId":"","doi":"10.1023/A:1026071317995"},{"reference":"Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. 2024. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 112: 108176.
","pubmedId":"39181100","doi":""},{"reference":"Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S, Oakeshott JG. 2016. Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Curr Opin Insect Sci 13: 70-76.
","pubmedId":"27436555","doi":""},{"reference":"Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, et al., Haeussler M. 2024. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res 52(D1): D1082-D1088.
","pubmedId":"37953330","doi":""},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.
","pubmedId":"24227676","doi":""},{"reference":"Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova MV, et al., Feyereisen R. 2002. Evolution of supergene families associated with insecticide resistance. Science 298(5591): 179-81.
","pubmedId":"12364796","doi":""},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Res 11: 1579.
","pubmedId":"37854289","doi":""},{"reference":"Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, et al., Schneider DJ. 2011. Creating a buzz about insect genomes. Science 331(6023): 1386.
","pubmedId":"21415334","doi":""},{"reference":"Russo CA, Takezaki N, Nei M. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12(3): 391-404.
","pubmedId":"7739381","doi":""},{"reference":"Stump AD, Jablonski SE, Bouton L, Wilder JA. 2011. Distribution and mechanism of α-amanitin tolerance in mycophagous Drosophila (Diptera: Drosophilidae). Environ Entomol 40(6): 1604-12.
","pubmedId":"22217779","doi":""},{"reference":"Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21(1): 36-44.
","pubmedId":"12949132","doi":""},{"reference":"Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, et al., Micklos DA. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One 14(10): e0224086.
","pubmedId":"31658277","doi":""},{"reference":"Threlfall J, Blaxter M. 2021. Launching the Tree of Life Gateway. Wellcome Open Res 6: 125.
","pubmedId":"34095514","doi":""},{"reference":"Werner T, Liu G, Kang D, Ekengren S, Steiner H, Hultmark D. 2000. A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster. Proc Natl Acad Sci U S A 97(25): 13772-7.
","pubmedId":"11106397","doi":""},{"reference":"Williams E, Chialvo P, Scott Chialvo C. 2026. Gene model for the ortholog of GstO3 in Drosophila dunni. MicroPubl Biol 2026: 10.17912/micropub.biology.002110.
","pubmedId":"42294398","doi":""}],"title":"Gene model for the ortholog of PGRP-SB1 in Drosophila funebris
","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"c9248d59-1cb0-4d1a-81b0-ab0ab3ea5723","decision":"accept","abstract":"We developed a gene model for the Peptidoglycan recognition protein SB1 ortholog (PGRP-SB1) in the ASM1890182v1 Genome Assembly (GenBank Accession: GCA_018901825.1) of Drosophila funebris. This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans-tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the Genomics Education Partnership. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. FlyBase is supported by grants: NHGRI U41HG000739 and U24HG010859, UK Medical Research Council MR/W024233/1, NSF 2035515 and 2039324, BBSRC BB/T014008/1, and Wellcome Trust PLM13398.
","authors":[{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_reviewEditing","dataCuration"],"email":"mollymcdonaald@gmail.com","firstName":"Molly","lastName":"McDonald","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0009-9559-3825"},{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_reviewEditing","validation"],"email":"chialvop@appstate.edu","firstName":"Pablo","lastName":"Chialvo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-3150-3167"},{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["conceptualization","supervision","validation","writing_originalDraft"],"email":"chialvoch@appstate.edu","firstName":"Clare","lastName":"Scott Chialvo","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9029-3593"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[{"description":"Zipped archive containing FASTA, PEP, and GFF
","doi":"10.22002/w8r9v-73q82","resourceType":"Dataset","name":"Dfun_PGRP-SB1_Model.tar.gz","url":"https://portal.micropublication.org/uploads/27c75a356476fe1293acfcf00dfeee09.gz"}],"funding":"This gene annotation project was funded by Nation Science Foundation grants DEB-1737869 (PI LKR, CoPI CSC) and DBI-2217912 (PI CSC). The Genomics Education Partnership (GEP; https://thegep.org/), which supports this project, is funded by the National Science Foundation (1915544; PI LKR) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517; PI LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.
","image":{"url":"https://portal.micropublication.org/uploads/a8e4e3f22fcf13fa78997e0a68944a1e.jpg"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for PGRP-SB1 in Drosophila melanogaster and Drosophila funebris. Thin underlying arrows indicate which DNA strand the target gene–PGRP-SB1–is located on in D. melanogaster (top) and D. funebris (bottom). The thin arrows pointing to the left indicate that PGRP-SB1 is on the negative strand in both D. melanogaster and D. funebris. The wide gene arrows pointing in the same direction as PGRP-SB1 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of PGRP-SB1 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. funebris indicate orthology to the corresponding gene in D. melanogaster, while black gene arrows indicate non-orthology and grey gene arrows indicate that the gene is present in both neighborhoods but not syntenic. Gene symbols given in the D. funebris gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. funebris. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of PGRP-SB1 in D. funebris are displayed in the User Supplied Track (red); coding sequences (CDS) are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Coding Regions Predicted by Augustus (dark blue), GeMoMa (teal), and NSCAN PASA-EST (dark green), and RNA-Seq from mixed sex adult flies (brown; alignment of Illumina RNA-Seq reads from D. funebris – Erlenbach et al., 2023). (C) Dot Plot of PGRP-SB1-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. funebris (y-axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. Line breaks in the dot plot indicate areas of with low sequence identity between species. One longer break is present that extends across all of CDS 1 and the beginning of CDS 2 (dark purple box – a). A smaller break is also present towards the end of CDS 2 (yellow box – b). (D) Idiosyncrasies in protein alignment. The protein model contains one longer break and a shorter break that indicate areas of low sequence identity. In the longer break that extends across all of CDS 1 and into CDS 2 (dark purple box – a), only two of the 25 amino acids are highly dissimilar. There is one fewer amino acid in CDS 1 of D. funebris, and an insertion of three amino acids is present at the beginning of CDS 2 of D. funebris. The shorter break that occurs towards the end of CDS 2 (yellow box – b) spans a region of 11 amino acids, only one of which is highly dissimilar.
","imageTitle":"Genomic neighborhood and gene model for PGRP-SB1 in D. funebris
","methods":"The annotation methods used in this project are adapted from those described in Rele et al. (2023), which includes algorithms, database versions, and citations for the complete annotation process developed for the Pathways Project. The methods for the current project are detailed in brief below with notes on significant differences between this protocol and the one described in Rele et al. (2023). The students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent et al., 2002; Raney et al., 2024) to examine the genomic neighborhood of their reference detoxification gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students obtain the protein sequence for the D. melanogaster target gene for a given isoform and use a tblastn search of the sequence against their target Drosophila species genome assembly (D. funebris (GCA_018901825.1 – Kim et al., 2013)) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify the putative ortholog location. Students compare the genomic neighborhood of the putative ortholog to that of the reference gene in D. melanogaster. This local synteny analysis includes a minimum of two upstream and downstream genes relative to the potential ortholog. As no RefSeq protein data is available for these species, comparisons are based on gene predictions that correlate with gene expression data in the putative ortholog neighborhood. Using the multiple alignment tracks feature in the Genome Browser, students examine other sets of genomic evidence, including Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Augustus, NSCAN PASA-EST), and mixed sex RNA-Seq adult expression data from the target species generated by Erlenbach et al. (2023; https://doi.org/10.5061/dryad.hdr7sqvq2). Information on the genomic structure information (e.g., CDSs, intron-exon number, number of isoforms) for the reference gene in D. melanogaster is retrieved using Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). To determine approximate splice sites within the target gene, a tblastn search using the CDSs from the D. melanogaster reference gene against the putative ortholog location (10kb up- and downstream of the target gene prediction). Coordinates of the CDS(s) are refined by examining aligned RNA-Seq data, identifying canonical splice site sequences, and ensuring the maintenance of an open reading frame. Students confirm the biological validity of their target gene model using the FlySeq Gene Model Checker (https://gander2.wustl.edu/~wilson/genechecker-flyseq/), which compares the hypothesized target gene model's structure and translated sequence against the D. melanogaster reference gene. At least two independent models for this gene are generated. These models are reconciled by a third independent researcher to produce the final model presented here. Note: comparison of 5' and 3' UTR sequence information is not included in this GEP CURE protocol.
","reagents":"","patternDescription":"This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org) for Course-based Undergraduate Research Experience (CURE). The following information in quotes may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster detoxification genes. “Within insects, the process of detoxifying xenobiotics and host secondary metabolites is a three-phase process that involves functionalization, conjugation, and excretion of these compounds. Expansions of known detoxification gene families (e.g., cytochrome P450s) is associated with diet breadth and insecticide resistance (Ranson et al., 2002; Després et al., 2007; Rane et al., 2016). With the increasing availability of high-quality genomes for non-model organisms, including Drosophila species beyond D. melanogaster, it is now possible to perform large scale comparative studies (Robinson et al., 2011; Kim et al., 2021; Threfall and Baxter, 2021). Careful manual annotation and curation of gene models can improve upon computational gene predictions in non-model species, which aids the accuracy of studies on gene and genome evolution (Mudge and Harrow, 2016; Tello-Ruiz et al., 2019). To aid in these annotations, the Genomics Education Partnership (thegep.org) developed a curriculum involving web-based tools that allow undergraduates to engage in authentic course-based research focused on manually annotating genes in non-model species (Rele et al., 2023). The orthologous gene models, including the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The gene ortholog described here in D. funebris for Peptidoglycan recognition protein SB1 (PGRP-SB1), a member of the peptidoglycan recognition protein family that contributes to the innate immune system of insects, was characterized as part of a developing dataset for a comparative study of detoxification gene families in the immigrans-tripunctata radiation of the genus Drosophila.” (Williams et al., 2026) Drosophila funebris (Fabricius, 1787) is a member of the funebris species group, which occurs in the immigrans-tripunctata radiation of the Drosophila subgenus (Bächli, 2005; ICZN, 2010). It is also the type species of the genus Drosophila. This species is a globally distributed human commensal (Grimaldi, 2022). While D. funebris feeds on shelf fungi and fruit (Kimura et al., 1977; Prigent et al., 2003), it does not tolerate the mushroom toxin α-amanitin (Stump et al., 2011; Erlenbach et al., 2023). |
When considering the detoxification of xenobiotics, the focus is often directed towards genes that produce detoxification enzymes. A growing body of work is beginning to highlight the role of genes in the insect's innate immune system in metabolizing these toxic compounds (Bartling et al., 2021; Jiang et al., 2021; Rahmat et al., 2024). One component of the innate immune system, peptidoglycan recognition proteins (PGRP), are pattern recognition molecules that detect molecular patterns found in pathogens but absent in the host organism (Akira et al., 2006; Lemaitre and Hoffman, 2007). Within Drosophila melanogaster, Werner et al. (2000) identified 12 PGRPs. These proteins are split into two subgroups (long and short) based on their transcript size, cellular location, and function (Werner et al., 2000). Peptidoglycan recognition protein SB1 (PGRP-SB1) is a short PGRP (Werner et al., 2000). It is an amidase that exhibits antibacterial activity against peptidoglycans that possess a diaminopimelic acid residue (Mellroth and Steiner, 2006). When Drosophila flies are exposed to wasp, mite, or nematode parasites, the expression of this gene is increased (Benoit et al., 2020). In addition, exposure to sublethal doses of six insecticides also increased the expression of PGRP-SB1 (Gao et al., 2021).
We propose a gene model for the D. funebris ortholog of the D. melanogaster Peptidoglycan recognition protein SB1 (PGRP-SB1) gene. The genomic region of the ortholog corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 in the ASM1890182v1 Genome Assembly of D. funebris (GCA_018901825.1- Kim et al. 2021). This model is based on mixed sex, adult RNA-Seq data from D. funebris (Erlenbach et al. 2023; https://doi.org/10.5061/dryad.hdr7sqvq2) and PGRP-SB1 in D. melanogaster using FlyBase release FB2024_02 (GCA_000001215.4; Gramates et al., 2022; Jenkins et al., 2022; Larkin et al., 2021).
Synteny
The reference gene, PGRP-SB1, occurs on chromosome 3L in D. melanogaster and is flanked upstream by Dead box protein 73D (Dbp73D) and CG9701 and downstream by Peptidoglycan recognition protein SB2 (PGRP-SB2) and CG13026. The tblastn search of D. melanogaster PGRP-SB1-PA (query) against the D. funebris (GenBank Accession: GCA_018901825.1 Genome Assembly database (subject) placed the putative ortholog of PGRP-SB1 within contig_693 (JAEIFK010000688) which corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 (E-value: 3.00e-113; percent identity: 78.2%; query coverage: 98% as determined by blastp). The putative ortholog is flanked upstream by Augustus gene predictions JAEIFK010000688.g513.t1 and JAEIFK010000688.g514.t1, which correspond to Dbp73D and CG9701 in D. melanogaster (E-value: 0.0 and 0.0; identity: 66.47% and 88.70%, respectively, as determined by blastp; Figure 1A; Altschul et al., 1990). The putative ortholog of PGRP-SB1 is flanked downstream by JAEIFK010000688.g511.t1 and JAEIFK010000688.g510.t1, which correspond to CG13026 and Disabled (Dab) in D. melanogaster (E-value: 1.00e-13 and 0.0 identity: 52.75% and 68.16%, respectively, as determined by blastp). Dab is the third gene downstream of the target gene, PGRP-SB1, in D. melanogaster. The putative ortholog assignment for PGRP-SB1 in D. funebris is supported by the following evidence: The gene predictions surrounding the PGRP-SB1 ortholog are all orthologous to the genes at the same locus in D. melanogaster except for the loss of the PGRP-SB2 gene, gene expression data corresponds with each prediction, and local synteny is almost entirely conserved, supported by E-values and percent identities, so we conclude that JAEIFK010000688.g512.t1 is an ortholog of PGRP-SB1 in D. funebris (Figure 1A).
Protein Model
PGRP-SB1 in D. funebris has 2 coding sequences (CDS) within the genome sequence. The only unique protein sequence (PGRP-SB1-PA) is translated from 1 mRNA isoform (PGRP-SB1-RA; Figure 1B). Relative to the ortholog in D. melanogaster, the CDS number and protein isoform count are conserved. The sequence of PGRP-SB1-PA in D. funebris has 78.1% identity (89.1% similarity) with the protein-coding isoform PGRP-SB1-PA in D. melanogaster, as determined by blastp (Figure 1C). This level of divergence is not surprising given that D. funebris and D. melanogaster belong to two separate subgenera (Drosophila and Sophophora respectively) that diverged approximately 45-60 MYA (Russo et al., 1995; Tamura et al., 2004; Obbard et al., 2012). Coordinates of this curated gene model are archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"reference":"Akira S, Uematsu S, Takeuchi O. 2006. Pathogen recognition and innate immunity. Cell 124(4): 783-801.
","pubmedId":"16497588","doi":""},{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.
","pubmedId":"2231712","doi":""},{"reference":"Bächli, G. (2005) Taxodros: The database on taxonomy of Drosophilidae, version February 2026, last accessed 28 May 2026. https://taxodros.uzh.ch/
","pubmedId":"","doi":""},{"reference":"Bartling MT, Thümecke S, Russert JH, Vilcinskas A, Lee KZ. 2021. Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees. Sci Rep 11(1): 6819.
","pubmedId":"33767272","doi":""},{"reference":"Benoit JB, Bose J, Bailey ST, Polak M. 2020. Interactions with ectoparasitic mites induce host metabolic and immune responses in flies at the expense of reproduction-associated factors. Parasitology 147(11): 1196-1205.
","pubmedId":"32498733","doi":""},{"reference":"Després L, David JP, Gallet C. 2007. The evolutionary ecology of insect resistance to plant chemicals. Trends Ecol Evol 22(6): 298-307.
","pubmedId":"17324485","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.
","pubmedId":"17994087","doi":""},{"reference":"Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone SA, Reed LK, Dyer KA, Scott Chialvo CH. 2023. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 13(12): e10736.
","pubmedId":"38099137","doi":""},{"reference":"Fabricius JC, Metcalf Collection (North Carolina State University)., Tippmann Collection (North Carolina State University).. 1787. Mantissa insectorum sistens eorum species nuper detectas adiectis characteribus genericis, differentiis specificis, emendationibus, observationibus, Ioh. Christ. Fabricii.. : 10.5962/bhl.title.36471.
","pubmedId":"","doi":"10.5962/bhl.title.36471"},{"reference":"Gao Y, Kim JH, Jeong IH, Clark JM, Lee SH. 2021. Transcriptomic identification and characterization of genes commonly responding to sublethal concentrations of six different insecticides in the common fruit fly, Drosophila melanogaster. Pestic Biochem Physiol 175: 104852.
","pubmedId":"33993970","doi":""},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al., the FlyBase Consortium. 2022. FlyBase: a guided tour of highlighted features. Genetics 220(4): 10.1093/genetics/iyac035.
","pubmedId":"35266522","doi":""},{"reference":"Grimaldi DA. 2022. The Drosophila funebris Species Group in North America (Diptera: Drosophilidae). American Museum Novitates 2022: 10.1206/3988.1.
","pubmedId":"","doi":"10.1206/3988.1"},{"reference":"ICZN. (2010) Opinion 2245 (Case 3407): Drosophila Fallén, 1823 (Insecta, Diptera): Drosophila funebris Fabricius, 1787 is maintained as the type species. The Bulletin of Zoological Nomenclature 67(1), 106-115.
","pubmedId":"","doi":"10.21805/bzn.v67i1.a14"},{"reference":"Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.
","pubmedId":"35980571","doi":""},{"reference":"Jiang DL, Ding JH, Liu ZX, Shao ZM, Liang XH, Wang J, Wu FA, Sheng S. 2021. A role of peptidoglycan recognition protein in mediating insecticide detoxification in Glyphodes pyloalis. Arch Insect Biochem Physiol 108(3): e21842.
","pubmedId":"34499777","doi":""},{"reference":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6): 996-1006.
","pubmedId":"12045153","doi":""},{"reference":"Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, et al., Petrov DA. 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife 10: 10.7554/eLife.66405.
","pubmedId":"34279216","doi":""},{"reference":"Kimura M, Toda M, Beppu K, Watabe H. (1977) Breeding sites of Drosophilid flies in and near Sapporo northern Japan, with supplementary notes on adult feeding habits. Japanese Journal of Entomology 45: 571-582.
","pubmedId":"","doi":""},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.
","pubmedId":"33219682","doi":""},{"reference":"Lemaitre B, Hoffmann J. 2007. The host defense of Drosophila melanogaster. Annu Rev Immunol 25: 697-743.
","pubmedId":"17201680","doi":""},{"reference":"Mellroth P, Steiner H. 2006. PGRP-SB1: an N-acetylmuramoyl L-alanine amidase with antibacterial activity. Biochem Biophys Res Commun 350(4): 994-9.
","pubmedId":"17046713","doi":""},{"reference":"Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.
","pubmedId":"27773922","doi":""},{"reference":"Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM. 2012. Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol 29(11): 3459-73.
","pubmedId":"22683811","doi":""},{"reference":"Prigent Sp, Renard E, Cariou ML. 2003. Electrophoretic Mobility of Amylase in Drosophilids Indicates Adaptation to Ecological Diversity. Genetica 119: 133-145.
","pubmedId":"","doi":"10.1023/A:1026071317995"},{"reference":"Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. 2024. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 112: 108176.
","pubmedId":"39181100","doi":""},{"reference":"Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S, Oakeshott JG. 2016. Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Curr Opin Insect Sci 13: 70-76.
","pubmedId":"27436555","doi":""},{"reference":"Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, et al., Haeussler M. 2024. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res 52(D1): D1082-D1088.
","pubmedId":"37953330","doi":""},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.
","pubmedId":"24227676","doi":""},{"reference":"Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova MV, et al., Feyereisen R. 2002. Evolution of supergene families associated with insecticide resistance. Science 298(5591): 179-81.
","pubmedId":"12364796","doi":""},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Res 11: 1579.
","pubmedId":"37854289","doi":""},{"reference":"Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, et al., Schneider DJ. 2011. Creating a buzz about insect genomes. Science 331(6023): 1386.
","pubmedId":"21415334","doi":""},{"reference":"Russo CA, Takezaki N, Nei M. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12(3): 391-404.
","pubmedId":"7739381","doi":""},{"reference":"Stump AD, Jablonski SE, Bouton L, Wilder JA. 2011. Distribution and mechanism of α-amanitin tolerance in mycophagous Drosophila (Diptera: Drosophilidae). Environ Entomol 40(6): 1604-12.
","pubmedId":"22217779","doi":""},{"reference":"Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21(1): 36-44.
","pubmedId":"12949132","doi":""},{"reference":"Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, et al., Micklos DA. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One 14(10): e0224086.
","pubmedId":"31658277","doi":""},{"reference":"Threlfall J, Blaxter M. 2021. Launching the Tree of Life Gateway. Wellcome Open Res 6: 125.
","pubmedId":"34095514","doi":""},{"reference":"Werner T, Liu G, Kang D, Ekengren S, Steiner H, Hultmark D. 2000. A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster. Proc Natl Acad Sci U S A 97(25): 13772-7.
","pubmedId":"11106397","doi":""},{"reference":"Williams E, Chialvo P, Scott Chialvo C. 2026. Gene model for the ortholog of GstO3 in Drosophila dunni. MicroPubl Biol 2026: 10.17912/micropub.biology.002110.
","pubmedId":"42294398","doi":""}],"title":"Gene model for the ortholog of PGRP-SB1 in Drosophila funebris
","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":"1783320835337"}]},{"id":"43abbbdc-0624-49c8-be8b-20346467d351","decision":"publish","abstract":"We developed a gene model for the Peptidoglycan recognition protein SB1 ortholog (PGRP-SB1) in the ASM1890182v1 Genome Assembly (GenBank Accession: GCA_018901825.1) of Drosophila funebris. This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans-tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the Genomics Education Partnership. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. FlyBase is supported by grants: NHGRI U41HG000739 and U24HG010859, UK Medical Research Council MR/W024233/1, NSF 2035515 and 2039324, BBSRC BB/T014008/1, and Wellcome Trust PLM13398.
","authors":[{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["formalAnalysis","investigation","writing_reviewEditing","dataCuration"],"email":"mollymcdonaald@gmail.com","firstName":"Molly","lastName":"McDonald","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0009-9559-3825"},{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["investigation","formalAnalysis","writing_reviewEditing","validation"],"email":"chialvop@appstate.edu","firstName":"Pablo","lastName":"Chialvo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0009-0001-3150-3167"},{"affiliations":["Appalachian State University, Boone, North Carolina USA"],"departments":["Biology"],"credit":["conceptualization","supervision","validation","writing_originalDraft"],"email":"chialvoch@appstate.edu","firstName":"Clare","lastName":"Scott Chialvo","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9029-3593"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":null},"extendedData":[{"description":"Zipped archive containing FASTA, PEP, and GFF
","doi":"10.22002/w8r9v-73q82","resourceType":"Dataset","name":"Dfun_PGRP-SB1_Model.tar.gz","url":"https://portal.micropublication.org/uploads/27c75a356476fe1293acfcf00dfeee09.gz"}],"funding":"This gene annotation project was funded by Nation Science Foundation grants DEB-1737869 (PI LKR, CoPI CSC) and DBI-2217912 (PI CSC). The Genomics Education Partnership (GEP; https://thegep.org/), which supports this project, is funded by the National Science Foundation (1915544; PI LKR) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517; PI LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.
","image":{"url":"https://portal.micropublication.org/uploads/a8e4e3f22fcf13fa78997e0a68944a1e.jpg"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for PGRP-SB1 in Drosophila melanogaster and Drosophila funebris. Thin underlying arrows indicate which DNA strand the target gene–PGRP-SB1–is located on in D. melanogaster (top) and D. funebris (bottom). The thin arrows pointing to the left indicate that PGRP-SB1 is on the negative strand in both D. melanogaster and D. funebris. The wide gene arrows pointing in the same direction as PGRP-SB1 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of PGRP-SB1 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. funebris indicate orthology to the corresponding gene in D. melanogaster, while black gene arrows indicate non-orthology and grey gene arrows indicate that the gene is present in both neighborhoods but not syntenic. Gene symbols given in the D. funebris gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. funebris. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of PGRP-SB1 in D. funebris are displayed in the User Supplied Track (red); coding sequences (CDS) are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Coding Regions Predicted by Augustus (dark blue), GeMoMa (teal), and NSCAN PASA-EST (dark green), and RNA-Seq from mixed sex adult flies (brown; alignment of Illumina RNA-Seq reads from D. funebris – Erlenbach et al., 2023). (C) Dot Plot of PGRP-SB1-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. funebris (y-axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. Line breaks in the dot plot indicate areas of with low sequence identity between species. One longer break is present that extends across all of CDS 1 and the beginning of CDS 2 (dark purple box – a). A smaller break is also present towards the end of CDS 2 (yellow box – b). (D) Idiosyncrasies in protein alignment. The protein model contains one longer break and a shorter break that indicate areas of low sequence identity. In the longer break that extends across all of CDS 1 and into CDS 2 (dark purple box – a), only two of the 25 amino acids are highly dissimilar. There is one fewer amino acid in CDS 1 of D. funebris, and an insertion of three amino acids is present at the beginning of CDS 2 of D. funebris. The shorter break that occurs towards the end of CDS 2 (yellow box – b) spans a region of 11 amino acids, only one of which is highly dissimilar.
","imageTitle":"Genomic neighborhood and gene model for PGRP-SB1 in D. funebris
","methods":"The annotation methods used in this project are adapted from those described in Rele et al. (2023), which includes algorithms, database versions, and citations for the complete annotation process developed for the Pathways Project. The methods for the current project are detailed in brief below with notes on significant differences between this protocol and the one described in Rele et al. (2023). The students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent et al., 2002; Raney et al., 2024) to examine the genomic neighborhood of their reference detoxification gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students obtain the protein sequence for the D. melanogaster target gene for a given isoform and use a tblastn search of the sequence against their target Drosophila species genome assembly (D. funebris (GCA_018901825.1 – Kim et al., 2013)) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify the putative ortholog location. Students compare the genomic neighborhood of the putative ortholog to that of the reference gene in D. melanogaster. This local synteny analysis includes a minimum of two upstream and downstream genes relative to the potential ortholog. As no RefSeq protein data is available for these species, comparisons are based on gene predictions that correlate with gene expression data in the putative ortholog neighborhood. Using the multiple alignment tracks feature in the Genome Browser, students examine other sets of genomic evidence, including Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Augustus, NSCAN PASA-EST), and mixed sex RNA-Seq adult expression data from the target species generated by Erlenbach et al. (2023; https://doi.org/10.5061/dryad.hdr7sqvq2). Information on the genomic structure information (e.g., CDSs, intron-exon number, number of isoforms) for the reference gene in D. melanogaster is retrieved using Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). To determine approximate splice sites within the target gene, a tblastn search using the CDSs from the D. melanogaster reference gene against the putative ortholog location (10kb up- and downstream of the target gene prediction). Coordinates of the CDS(s) are refined by examining aligned RNA-Seq data, identifying canonical splice site sequences, and ensuring the maintenance of an open reading frame. Students confirm the biological validity of their target gene model using the FlySeq Gene Model Checker (https://gander2.wustl.edu/~wilson/genechecker-flyseq/), which compares the hypothesized target gene model's structure and translated sequence against the D. melanogaster reference gene. At least two independent models for this gene are generated. These models are reconciled by a third independent researcher to produce the final model presented here. Note: comparison of 5' and 3' UTR sequence information is not included in this GEP CURE protocol.
","reagents":"","patternDescription":"This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org) for Course-based Undergraduate Research Experience (CURE). The following information in quotes may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster detoxification genes. “Within insects, the process of detoxifying xenobiotics and host secondary metabolites is a three-phase process that involves functionalization, conjugation, and excretion of these compounds. Expansions of known detoxification gene families (e.g., cytochrome P450s) is associated with diet breadth and insecticide resistance (Ranson et al., 2002; Després et al., 2007; Rane et al., 2016). With the increasing availability of high-quality genomes for non-model organisms, including Drosophila species beyond D. melanogaster, it is now possible to perform large scale comparative studies (Robinson et al., 2011; Kim et al., 2021; Threfall and Baxter, 2021). Careful manual annotation and curation of gene models can improve upon computational gene predictions in non-model species, which aids the accuracy of studies on gene and genome evolution (Mudge and Harrow, 2016; Tello-Ruiz et al., 2019). To aid in these annotations, the Genomics Education Partnership (thegep.org) developed a curriculum involving web-based tools that allow undergraduates to engage in authentic course-based research focused on manually annotating genes in non-model species (Rele et al., 2023). The orthologous gene models, including the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The gene ortholog described here in D. funebris for Peptidoglycan recognition protein SB1 (PGRP-SB1), a member of the peptidoglycan recognition protein family that contributes to the innate immune system of insects, was characterized as part of a developing dataset for a comparative study of detoxification gene families in the immigrans-tripunctata radiation of the genus Drosophila.” (Williams et al., 2026) Drosophila funebris (Fabricius, 1787) is a member of the funebris species group, which occurs in the immigrans-tripunctata radiation of the Drosophila subgenus (Bächli, 2005; ICZN, 2010). It is also the type species of the genus Drosophila. This species is a globally distributed human commensal (Grimaldi, 2022). While D. funebris feeds on shelf fungi and fruit (Kimura et al., 1977; Prigent et al., 2003), it does not tolerate the mushroom toxin α-amanitin (Stump et al., 2011; Erlenbach et al., 2023). |
When considering the detoxification of xenobiotics, the focus is often directed towards genes that produce detoxification enzymes. A growing body of work is beginning to highlight the role of genes in the insect's innate immune system in metabolizing these toxic compounds (Bartling et al., 2021; Jiang et al., 2021; Rahmat et al., 2024). One component of the innate immune system, peptidoglycan recognition proteins (PGRP), are pattern recognition molecules that detect molecular patterns found in pathogens but absent in the host organism (Akira et al., 2006; Lemaitre and Hoffman, 2007). Within Drosophila melanogaster, Werner et al. (2000) identified 12 PGRPs. These proteins are split into two subgroups (long and short) based on their transcript size, cellular location, and function (Werner et al., 2000). Peptidoglycan recognition protein SB1 (PGRP-SB1) is a short PGRP (Werner et al., 2000). It is an amidase that exhibits antibacterial activity against peptidoglycans that possess a diaminopimelic acid residue (Mellroth and Steiner, 2006). When Drosophila flies are exposed to wasp, mite, or nematode parasites, the expression of this gene is increased (Benoit et al., 2020). In addition, exposure to sublethal doses of six insecticides also increased the expression of PGRP-SB1 (Gao et al., 2021).
We propose a gene model for the D. funebris ortholog of the D. melanogaster Peptidoglycan recognition protein SB1 (PGRP-SB1) gene. The genomic region of the ortholog corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 in the ASM1890182v1 Genome Assembly of D. funebris (GCA_018901825.1- Kim et al. 2021). This model is based on mixed sex, adult RNA-Seq data from D. funebris (Erlenbach et al. 2023; https://doi.org/10.5061/dryad.hdr7sqvq2) and PGRP-SB1 in D. melanogaster using FlyBase release FB2024_02 (GCA_000001215.4; Gramates et al., 2022; Jenkins et al., 2022; Larkin et al., 2021).
Synteny
The reference gene, PGRP-SB1, occurs on chromosome 3L in D. melanogaster and is flanked upstream by Dead box protein 73D (Dbp73D) and CG9701 and downstream by Peptidoglycan recognition protein SB2 (PGRP-SB2) and CG13026. The tblastn search of D. melanogaster PGRP-SB1-PA (query) against the D. funebris (GenBank Accession: GCA_018901825.1 Genome Assembly database (subject) placed the putative ortholog of PGRP-SB1 within contig_693 (JAEIFK010000688) which corresponds to the Augustus gene prediction JAEIFK010000688.g512.t1 (E-value: 3.00e-113; percent identity: 78.2%; query coverage: 98% as determined by blastp). The putative ortholog is flanked upstream by Augustus gene predictions JAEIFK010000688.g513.t1 and JAEIFK010000688.g514.t1, which correspond to Dbp73D and CG9701 in D. melanogaster (E-value: 0.0 and 0.0; identity: 66.47% and 88.70%, respectively, as determined by blastp; Figure 1A; Altschul et al., 1990). The putative ortholog of PGRP-SB1 is flanked downstream by JAEIFK010000688.g511.t1 and JAEIFK010000688.g510.t1, which correspond to CG13026 and Disabled (Dab) in D. melanogaster (E-value: 1.00e-13 and 0.0 identity: 52.75% and 68.16%, respectively, as determined by blastp). Dab is the third gene downstream of the target gene, PGRP-SB1, in D. melanogaster. The putative ortholog assignment for PGRP-SB1 in D. funebris is supported by the following evidence: The gene predictions surrounding the PGRP-SB1 ortholog are all orthologous to the genes at the same locus in D. melanogaster except for the loss of the PGRP-SB2 gene, gene expression data corresponds with each prediction, and local synteny is almost entirely conserved, supported by E-values and percent identities, so we conclude that JAEIFK010000688.g512.t1 is an ortholog of PGRP-SB1 in D. funebris (Figure 1A).
Protein Model
PGRP-SB1 in D. funebris has 2 coding sequences (CDS) within the genome sequence. The only unique protein sequence (PGRP-SB1-PA) is translated from 1 mRNA isoform (PGRP-SB1-RA; Figure 1B). Relative to the ortholog in D. melanogaster, the CDS number and protein isoform count are conserved. The sequence of PGRP-SB1-PA in D. funebris has 78.1% identity (89.1% similarity) with the protein-coding isoform PGRP-SB1-PA in D. melanogaster, as determined by blastp (Figure 1C). This level of divergence is not surprising given that D. funebris and D. melanogaster belong to two separate subgenera (Drosophila and Sophophora respectively) that diverged approximately 45-60 MYA (Russo et al., 1995; Tamura et al., 2004; Obbard et al., 2012). Coordinates of this curated gene model are archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"reference":"Akira S, Uematsu S, Takeuchi O. 2006. Pathogen recognition and innate immunity. Cell 124(4): 783-801.
","pubmedId":"16497588","doi":""},{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215(3): 403-10.
","pubmedId":"2231712","doi":""},{"reference":"Bächli, G. (2005) Taxodros: The database on taxonomy of Drosophilidae, version February 2026, last accessed 28 May 2026. https://taxodros.uzh.ch/
","pubmedId":"","doi":""},{"reference":"Bartling MT, Thümecke S, Russert JH, Vilcinskas A, Lee KZ. 2021. Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees. Sci Rep 11(1): 6819.
","pubmedId":"33767272","doi":""},{"reference":"Benoit JB, Bose J, Bailey ST, Polak M. 2020. Interactions with ectoparasitic mites induce host metabolic and immune responses in flies at the expense of reproduction-associated factors. Parasitology 147(11): 1196-1205.
","pubmedId":"32498733","doi":""},{"reference":"Després L, David JP, Gallet C. 2007. The evolutionary ecology of insect resistance to plant chemicals. Trends Ecol Evol 22(6): 298-307.
","pubmedId":"17324485","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.
","pubmedId":"17994087","doi":""},{"reference":"Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone SA, Reed LK, Dyer KA, Scott Chialvo CH. 2023. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 13(12): e10736.
","pubmedId":"38099137","doi":""},{"reference":"Fabricius JC, Metcalf Collection (North Carolina State University)., Tippmann Collection (North Carolina State University).. 1787. Mantissa insectorum sistens eorum species nuper detectas adiectis characteribus genericis, differentiis specificis, emendationibus, observationibus, Ioh. Christ. Fabricii.. : 10.5962/bhl.title.36471.
","pubmedId":"","doi":"10.5962/bhl.title.36471"},{"reference":"Gao Y, Kim JH, Jeong IH, Clark JM, Lee SH. 2021. Transcriptomic identification and characterization of genes commonly responding to sublethal concentrations of six different insecticides in the common fruit fly, Drosophila melanogaster. Pestic Biochem Physiol 175: 104852.
","pubmedId":"33993970","doi":""},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al., the FlyBase Consortium. 2022. FlyBase: a guided tour of highlighted features. Genetics 220(4): 10.1093/genetics/iyac035.
","pubmedId":"35266522","doi":""},{"reference":"Grimaldi DA. 2022. The Drosophila funebris Species Group in North America (Diptera: Drosophilidae). American Museum Novitates 2022: 10.1206/3988.1.
","pubmedId":"","doi":"10.1206/3988.1"},{"reference":"ICZN. (2010) Opinion 2245 (Case 3407): Drosophila Fallén, 1823 (Insecta, Diptera): Drosophila funebris Fabricius, 1787 is maintained as the type species. The Bulletin of Zoological Nomenclature 67(1), 106-115.
","pubmedId":"","doi":"10.21805/bzn.v67i1.a14"},{"reference":"Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.
","pubmedId":"35980571","doi":""},{"reference":"Jiang DL, Ding JH, Liu ZX, Shao ZM, Liang XH, Wang J, Wu FA, Sheng S. 2021. A role of peptidoglycan recognition protein in mediating insecticide detoxification in Glyphodes pyloalis. Arch Insect Biochem Physiol 108(3): e21842.
","pubmedId":"34499777","doi":""},{"reference":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6): 996-1006.
","pubmedId":"12045153","doi":""},{"reference":"Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, et al., Petrov DA. 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife 10: 10.7554/eLife.66405.
","pubmedId":"34279216","doi":""},{"reference":"Kimura M, Toda M, Beppu K, Watabe H. (1977) Breeding sites of Drosophilid flies in and near Sapporo northern Japan, with supplementary notes on adult feeding habits. Japanese Journal of Entomology 45: 571-582.
","pubmedId":"","doi":""},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.
","pubmedId":"33219682","doi":""},{"reference":"Lemaitre B, Hoffmann J. 2007. The host defense of Drosophila melanogaster. Annu Rev Immunol 25: 697-743.
","pubmedId":"17201680","doi":""},{"reference":"Mellroth P, Steiner H. 2006. PGRP-SB1: an N-acetylmuramoyl L-alanine amidase with antibacterial activity. Biochem Biophys Res Commun 350(4): 994-9.
","pubmedId":"17046713","doi":""},{"reference":"Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.
","pubmedId":"27773922","doi":""},{"reference":"Obbard DJ, Maclennan J, Kim KW, Rambaut A, O'Grady PM, Jiggins FM. 2012. Estimating divergence dates and substitution rates in the Drosophila phylogeny. Mol Biol Evol 29(11): 3459-73.
","pubmedId":"22683811","doi":""},{"reference":"Prigent Sp, Renard E, Cariou ML. 2003. Electrophoretic Mobility of Amylase in Drosophilids Indicates Adaptation to Ecological Diversity. Genetica 119: 133-145.
","pubmedId":"","doi":"10.1023/A:1026071317995"},{"reference":"Rahmat NL, Zifruddin AN, Yusoff NS, Sulaiman S, Zainal Abidin CMR, Othman NW, Nor Muhammad NA, Hassan M. 2024. Transcriptome analysis reveals mechanisms of metabolic detoxification and immune responses following farnesyl acetate treatment in Metisa plana. Comput Biol Chem 112: 108176.
","pubmedId":"39181100","doi":""},{"reference":"Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S, Oakeshott JG. 2016. Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores? Curr Opin Insect Sci 13: 70-76.
","pubmedId":"27436555","doi":""},{"reference":"Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, et al., Haeussler M. 2024. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res 52(D1): D1082-D1088.
","pubmedId":"37953330","doi":""},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.
","pubmedId":"24227676","doi":""},{"reference":"Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova MV, et al., Feyereisen R. 2002. Evolution of supergene families associated with insecticide resistance. Science 298(5591): 179-81.
","pubmedId":"12364796","doi":""},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Res 11: 1579.
","pubmedId":"37854289","doi":""},{"reference":"Robinson GE, Hackett KJ, Purcell-Miramontes M, Brown SJ, Evans JD, Goldsmith MR, et al., Schneider DJ. 2011. Creating a buzz about insect genomes. Science 331(6023): 1386.
","pubmedId":"21415334","doi":""},{"reference":"Russo CA, Takezaki N, Nei M. 1995. Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12(3): 391-404.
","pubmedId":"7739381","doi":""},{"reference":"Stump AD, Jablonski SE, Bouton L, Wilder JA. 2011. Distribution and mechanism of α-amanitin tolerance in mycophagous Drosophila (Diptera: Drosophilidae). Environ Entomol 40(6): 1604-12.
","pubmedId":"22217779","doi":""},{"reference":"Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21(1): 36-44.
","pubmedId":"12949132","doi":""},{"reference":"Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, et al., Micklos DA. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One 14(10): e0224086.
","pubmedId":"31658277","doi":""},{"reference":"Threlfall J, Blaxter M. 2021. Launching the Tree of Life Gateway. Wellcome Open Res 6: 125.
","pubmedId":"34095514","doi":""},{"reference":"Werner T, Liu G, Kang D, Ekengren S, Steiner H, Hultmark D. 2000. A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster. Proc Natl Acad Sci U S A 97(25): 13772-7.
","pubmedId":"11106397","doi":""},{"reference":"Williams E, Chialvo P, Scott Chialvo C. 2026. Gene model for the ortholog of GstO3 in Drosophila dunni. MicroPubl Biol 2026: 10.17912/micropub.biology.002110.
","pubmedId":"42294398","doi":""}],"title":"Gene model for the ortholog of PGRP-SB1 in Drosophila funebris
","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]}]}},"species":{"species":[{"value":"acer saccharum","label":"Acer saccharum","imageSrc":"","imageAlt":"","mod":"TreeGenes","modLink":"https://treegenesdb.org","linkVariable":""},{"value":"achillea millefolium","label":"Achillea millefolium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"acinetobacter baylyi","label":"Acinetobacter baylyi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"actinobacteria bacterium","label":"Actinobacteria bacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adelges tsugae","label":"Adelges tsugae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"adenocaulon chilense","label":"Adenocaulon chilense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aedes japonicus","label":"Aedes japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aegorhinus vitulus","label":"Aegorhinus vitulus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alaimidae","label":"Alaimidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"allobates femoralis","label":"Allobates femoralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alnus glutinosa","label":"Alnus glutinosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa aestivalis","label":"Alosa aestivalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alosa pseudoharengus","label":"Alosa pseudoharengus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"alternaria alternata","label":"Alternaria alternata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"amynthas agrestis","label":"Amynthas Agrestis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma caninum","label":"Ancylostoma caninum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ancylostoma ceylanicum","label":"Ancylostoma ceylanicum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anemone multifida","label":"Anemone multifida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anguilla rostrata","label":"Anguilla rostrata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anisakis simplex","label":"Anisakis simplex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anomala albopilosa","label":"Anomala albopilosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"anthomyiidae sp","label":"Anthomyiidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arabidopsis","label":"Arabidopsis","imageSrc":"arabidopsis.png","imageAlt":"Arabidopsis graphic by Zoe Zorn CC BY 4.0","mod":"TAIR","modLink":"https://arabidopsis.org","linkVariable":""},{"value":"architeuthis dux","label":"Architeuthis dux","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arion vulgaris","label":"Arion vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"armeria","label":"Armeria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"artemia","label":"Artemia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"arthrobacter sp.","label":"Arthrobacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia","label":"Ascaridia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ascaridia galli","label":"Ascaridia galli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"asparagopsis taxiformis","label":"Asparagopsis taxiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"astatotilapia burtoni","label":"Astatotilapia burtoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"avena sativa","label":"Avena sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"aves","label":"Aves","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus","label":"Bacillus (firmicutes)","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus cereus","label":"Bacillus cereus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus mycoides","label":"Bacillus mycoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus subtilis","label":"Bacillus subtilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus thuringiensis","label":"Bacillus thuringiensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus toyonensis","label":"Bacillus toyonensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacillus wiedmannii","label":"Bacillus wiedmannii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteria","label":"Bacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bacteriophage","label":"Bacteriophage","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bactrocera","label":"Bactrocera sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"batrachospermum gelatinosum","label":"Batrachospermum gelatinosum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula lenta","label":"Betula lenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"betula nigra","label":"Betula nigra","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus dahlbohmii","label":"Bombus dahlbohmii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombus terrestris","label":"Bombus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bombyx mori","label":"Bombyx mori","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bos taurus","label":"Bos Taurus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brachygobius doriae","label":"Brachygobius doriae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica oleracea","label":"Brassica oleracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brassica rapa","label":"Brassica rapa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"brugia malayi","label":"Brugia malayi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"burkholderia thailandensis","label":"Burkholderia thailandensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"buttiauxella","label":"Buttiauxella","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis brenneri","label":"Caenorhabditis brenneri","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis briggsae","label":"Caenorhabditis briggsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"c. elegans","label":"Caenorhabditis elegans","imageSrc":"c-elegans.jpg","imageAlt":"C. elegans graphic by Zoe Zorn CC BY 4.0","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"caenorhabditis inopinata","label":"Caenorhabditis inopinata","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis japonica","label":"Caenorhabditis japonica","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis nigoni","label":"Caenorhabditis nigoni","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caenorhabditis remanei","label":"Caenorhabditis remanei","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"caenorhabditis tropicalis","label":"Caenorhabditis tropicalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus","label":"Calidifontibacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calidifontibacillus erzuremensis","label":"Calidifontibacillus erzuremensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"calliphora sp","label":"Calliphora sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caltha sagittata","label":"Caltha sagittata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cambarus latimanus","label":"Cambarus latimanus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"candida albicans","label":"Candida albicans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"canis familiaris","label":"Canis familiaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cannabis sativa","label":"Cannabis sativa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caretta caretta","label":"Caretta caretta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cassiopea xamachana","label":"Cassiopea xamachana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"caulobacter vibrioides","label":"Caulobacter vibrioides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cephalopods","label":"Cephalopoda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cerastium arvense","label":"Cerastium arvense","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceriodaphnia","label":"Ceriodaphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ceroglossus suturalis","label":"Ceroglossus suturalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chaetoceros","label":"Chaetoceros","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chamaecrista fasciculata","label":"Chamaecrista fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chilicola chalcidiformis","label":"Chilicola chalcidiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chitinimonas","label":"Chitinimonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chlamydomonas reinhardtii","label":"Chlamydomonas reinhardtii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chromobacterium","label":"Chromobacterium","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysemys picta","label":"Chrysemys picta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"chrysoperla rufilabris","label":"Chrysoperla rufilabris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"citrus","label":"Citrus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"clavibacter sp.","label":"Clavibacter sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"colinus virginianus","label":"Colinus virginianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crassostrea virginica","label":"Crassostrea virginica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"crithidia fasciculata","label":"Crithidia fasciculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cutibacterium acnes","label":"Cutibacterium acnes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"cyanobacteria","label":"Cyanobacteria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia","label":"Daphnia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"daphnia pulex","label":"Daphnia pulex","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera","label":"Diabrotica virgifera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"diabrotica virgifera virgifera virus 1","label":"Diabrotica virgifera virgifera virus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"d. discoideum","label":"Dictyostelium discoideum","imageSrc":"dicty.png","imageAlt":"D. discoideum","mod":"dictyBase","modLink":"http://dictybase.org","linkVariable":""},{"value":"diptera","label":"Diptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dotocryptus bellicosus","label":"Dotocryptus bellicosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drechmeria coniospora","label":"Drechmeria coniospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"drosophila","label":"Drosophila","imageSrc":"drosophila.png","imageAlt":"Drosophila graphic by Zoe Zorn CC BY 4.0","mod":"FlyBase","modLink":"https://flybase.org/doi/","linkVariable":"doi"},{"value":"dryopteris campyloptera","label":"Dryopteris campyloptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris expansa","label":"Dryopteris expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dryopteris intermedia","label":"Dryopteris intermedia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"dugesia dorotocephala","label":"Dugesia dorotocephala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"elasmobranchii","label":"Elasmobranchii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"embryophyta","label":"Embryophyta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enoploteuthis chunii","label":"Enoploteuthis chunii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterobacter aerogenes","label":"Enterobacter aerogenes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"enterococcus raffinosus","label":"Enterococcus raffinosus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"epichloë coenophiala","label":"Epichloë coenophiala","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"equus caballus","label":"Equus caballus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erigeron sp","label":"Erigeron sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eristalis","label":"Eristalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eruca vesicaria","label":"Eruca vesicaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erwinia carotovora","label":"Erwinia carotovora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"erythronium americanum","label":"Erythronium americanum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"escherichia coli","label":"Escherichia coli","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"eukaryota","label":"Eukaryotes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"felis catus","label":"Felis catus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella novicida","label":"Francisella novicida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"francisella tularensis","label":"Francisella tularensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fraxinus americana","label":"Fraxinus americana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fucus distichus","label":"Fucus distichus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"fungi","label":"Fungi","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gasteropelecus sp.","label":"Gasteropelecus sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"geranium sp","label":"Geranium sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"girardia","label":"Girardia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glaucomys volans","label":"Glaucomys volans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"glycine max","label":"Glycine max","imageSrc":"","imageAlt":"","mod":"Soybase","modLink":"https://soybase.org","linkVariable":""},{"value":"glyptemys insculpta","label":"Glyptemys insculpta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gossypium hirsutum","label":"Gossypium hirsutum","imageSrc":"","imageAlt":"","mod":"CottonGen","modLink":"https://www.cottongen.org/","linkVariable":""},{"value":"gromphadorhina portentosa","label":"Gromphadorhina portentosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"gryllodes sigillatus","label":"Gryllodes sigillatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"haliotis rufescens","label":"Haliotis rufescens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hepacivirus hominis","label":"Hepatitis C Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"herpes simplex virus type 1","label":"Herpes simplex virus type 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human","label":"Human","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"human coronavirus oc43","label":"Human coronavirus OC43","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydra vulgaris","label":"Hydra vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hydropsyche sp","label":"Hydropsyche sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hymenoptera","label":"Hymenoptera","imageSrc":"","imageAlt":"","mod":"Hymenoptera Genome Database","modLink":"https://hymenoptera.elsiklab.missouri.edu/","linkVariable":""},{"value":"hypochaeris radicata","label":"Hypochaeris radicata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"hypodynerus vespiformis","label":"Hypodynerus vespiformis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflaviridae","label":"Iflaviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"iflavuris","label":"Iflavirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ipomoea hederacea","label":"Ipomoea hederacea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera","label":"Ischnomera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ischnomera ruficollis","label":"Ischnomera ruficollis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"julidochromis marlieri","label":"Julidochromis marlieri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"juniperus virginiana","label":"Juniperus virginiana","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"kluyveromyces marxianus","label":"Kluyveromyces marxianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"l. casei","label":"L. casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lacticaseibacillus casei","label":"Lacticaseibacillus casei","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"larentiinae sp","label":"Larentiinae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"laurus nobilis","label":"Laurus nobilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lepidoptera","label":"Lepidoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"leucanthemum vulgare","label":"Leucanthemum vulgare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"linepithema humile","label":"Linepithema humile","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"liometopum occidentale","label":"Liometopum occidentale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lolium arundinaceum","label":"Lolium arundinaceum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbriculus variegatus","label":"Lumbriculus variegatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lumbricus terrestris","label":"Lumbricus terrestris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lupinus polyphyllus","label":"Lupinus polyphyllus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lycorma delicatula","label":"Lycorma delicatula","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"lynx rufus","label":"Lynx rufus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"magnaporthe oryzae","label":"Magnaporthe oryzae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mammalia","label":"Mammalia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"manihot esculenta","label":"Manihot esculenta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"medicago lupulina","label":"Medicago lupulina","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"meloidogyne","label":"Meloidogyne","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mimus polyglottos","label":"Mimus polyglottos","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"bryophyta","label":"Mosses","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mouse","label":"Mouse","imageSrc":"","imageAlt":"","mod":"MGI","modLink":"https://informatics.jax.org","linkVariable":""},{"value":"m. minutoides","label":"Mus minutoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"mycobacterium smegmatis","label":"Mycobacterium smegmatis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nakaseomyces glabratus","label":"Nakaseomyces glabratus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nauphoeta cinerea","label":"Nauphoeta cinerea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"neurospora","label":"Neurospora","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"n. benthamiana","label":"Nicotiana benthamiana","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/Nicotiana_benthamiana/genome","linkVariable":""},{"value":"nicotiana tabacum","label":"Nicotiana tabacum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae","label":"Noctuidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"noctuidae sp","label":"Noctuidae sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"nothobranchius furzeri","label":"Nothobranchius furzeri","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"onchocerca volvulus","label":"Onchocerca volvulus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"orconectes virilis","label":"Orconectes virilis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ormia ochracea","label":"Ormia ochracea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"o. sativa","label":"Oryza sativa","imageSrc":"","imageAlt":"","mod":"Gramene","modLink":"https://www.gramene.org/","linkVariable":""},{"value":"other","label":"Other","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"oxalis enneaphylla","label":"Oxalis enneaphylla","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paenarthrobacter nicotinovorans","label":"Paenarthrobacter nicotinovorans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea","label":"Pantoea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pantoea agglomerans","label":"Pantoea agglomerans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"papaver sp","label":"Papaver sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"paramecium bursaria","label":"Paramecium bursaria","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"partitiviridae","label":"Partitiviridae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pelodiscus sinensis","label":"Pelodiscus sinensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"perezia recurvata","label":"Perezia recurvata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"petromyzon marinus","label":"Petromyzon marinus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis","label":"Photinus pyralis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis associated partiti-like virus","label":"Photinus pyralis associated partiti-like virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"photinus pyralis iflavirus 1","label":"Photinus pyralis iflavirus 1","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"physcomitrium patens","label":"Physcomitrium patens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus strobus","label":"Pinus strobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pinus taeda","label":"Pinus taeda","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"platycheirus","label":"Platycheirus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"plectus sambesii","label":"Plectus sambesii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pogonomyrmex occidentalis","label":"Pogonomyrmex occidentalis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"poncirus trifoliata","label":"Poncirus trifoliata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"populus deltoides","label":"Populus deltoides","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"potato virus y","label":"Potato virus Y","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"primula magellanica","label":"Primula magellanica","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pristionchus pacificus","label":"Pristionchus pacificus","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"prunus persica","label":"Prunus persica","imageSrc":"","imageAlt":"","mod":"Genome Database for Rosaceae","modLink":"https://www.rosaceae.org/","linkVariable":""},{"value":"psalmopoeus iriminia","label":"Psalmopoeus iriminia","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudanabaena sp.","label":"Pseudanabaena sp.","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas","label":"Pseudomonas","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas aeruginosa","label":"Pseudomonas aeruginosa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas glycinae","label":"Pseudomonas glycinae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas putida","label":"Pseudomonas putida","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pseudomonas syringae","label":"Pseudomonas syringae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"pterophyllum scalare","label":"Pterophyllum scalare","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"python regius","label":"Python regius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"quercus macrocarpa","label":"Quercus macrocarpa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ralstonia solanacearum","label":"Ralstonia solanacearum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranitomeya imitator","label":"Ranitomeya imitator","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ranunculus peduncularis","label":"Ranunculus peduncularis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"rat","label":"Rat","imageSrc":"","imageAlt":"","mod":"RGD","modLink":"https://rgd.mcw.edu","linkVariable":""},{"value":"rheinheimera","label":"Rheinheimera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ribes rubrum","label":"Ribes rubrum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"sars-cov-2","label":"SARS-CoV-2","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. cerevisiae","label":"Saccharomyces cerevisiae","imageSrc":"yeast.png","imageAlt":"Yeast graphic by Zoe Zorn CC BY 4.0","mod":"SGD","modLink":"https://yeastgenome.org","linkVariable":""},{"value":"saccharomyces paradoxus","label":"Saccharomyces paradoxus ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. uvarum","label":"Saccharomyces uvarum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schistosoma","label":"Schistosoma","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"schizosaccharomyces japonicus","label":"Schizosaccharomyces japonicus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. pombe","label":"Schizosaccharomyces pombe","imageSrc":"pombe.png","imageAlt":"Pombe graphic by Zoe Zorn © Caltech","mod":"PomBase","modLink":"https://www.pombase.org/reference/PMID:","linkVariable":"pmId"},{"value":"schmidtea mediterranea","label":"Schmidtea mediterranea","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"senecio sp","label":"Senecio sp","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"simocephalus","label":"Simocephalus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"siraitia grosvenorii","label":"Siraitia grosvenorii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"solanum lycopersicum","label":"Solanum lycopersicum","imageSrc":"","imageAlt":"","mod":"Solgenomics Network","modLink":"https://solgenomics.net/organism/1/view/","linkVariable":""},{"value":"sorghum","label":"Sorghum","imageSrc":"","imageAlt":"","mod":"SorghumBase","modLink":"https://www.sorghumbase.org","linkVariable":""},{"value":"spiroplasma eriocheiris","label":"Spiroplasma eriocheiris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus aureus","label":"Staphylococcus aureus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"staphylococcus epidermidis","label":"Staphylococcus epidermidis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"steinernema carpocapsae","label":"Steinernema carpocapsae","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"https://wormbase.org","linkVariable":""},{"value":"steinernema hermaphroditum","label":"Steinernema hermaphroditum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"stenotrophomonas geniculata","label":"Stenotrophomonas geniculata","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus gordonii ","label":"Streptococcus gordonii ","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"streptococcus mutans","label":"Streptococcus mutans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":" streptococcus pneumoniae","label":"Streptococcus pneumoniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"s. purpuratus","label":"Strongylocentrotus purpuratus","imageSrc":"","imageAlt":"","mod":"Echinobase","modLink":"https://www.echinobase.org","linkVariable":""},{"value":"strongyloides ratti","label":"Strongyloides ratti","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"sulfolobus","label":"Sulfolobus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"symphoricarpos albus","label":"Symphoricarpos albus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syncirsodes","label":"Syncirsodes","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"synechococcus elongatus","label":"Synechococcus elongatus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"syrphidae","label":"Syrphidae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tarantobelus jeffdanielsi","label":"Tarantobelus jeffdanielsi","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"taraxacum officinale","label":"Taraxacum officinale","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tatochila theodice","label":"Tatochila theodice","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetrahymena","label":"Tetrahymena","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tetramorium immigrans","label":"Tetramorium immigrans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tomato brown rugose fruit virus","label":"ToBRFV","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trachemys scripta","label":"Trachemys scripta","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tribolium castaneum","label":"Tribolium castaneum","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichoptera","label":"Trichoptera","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trichuris muris","label":"Trichuris muris","imageSrc":"","imageAlt":"","mod":"WormBase","modLink":"www.wormbase.org","linkVariable":""},{"value":"trifolium repens","label":"Trifolium repens","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"trypoxylus dichotomus","label":"Trypoxylus dichotomus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"tsuga canadensis","label":"Tsuga canadensis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ulva expansa","label":"Ulva expansa","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"universal","label":"Universal","imageSrc":"","imageAlt":"","mod":null,"modLink":null,"linkVariable":null},{"value":"vargula hilgendorfii","label":"Vargula hilgendorfii","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"vespula vulgaris","label":"Vespula vulgaris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"virus","label":"Virus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"watasenia scintillans","label":"Watasenia scintillans","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"wolbachia pipientis","label":"Wolbachia pipientis","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"xenopus","label":"Xenopus","imageSrc":"xenopus.png","imageAlt":"Xenopus graphic by Zoe Zorn CC BY 4.0","mod":"XenBase","modLink":"https://xenbase.org","linkVariable":""},{"value":"xenorhabdus griffiniae","label":"Xenorhabdus griffiniae","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"yramea cytheris","label":"Yramea cytheris","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zaprionus indianus","label":"Zaprionus indianus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"zea mays","label":"Zea mays","imageSrc":"","imageAlt":"","mod":"MaizeGDB","modLink":"https://www.maizegdb.org","linkVariable":""},{"value":"zebrafish","label":"Zebrafish","imageSrc":"zebrafish.png","imageAlt":"Zebrafish graphic by Zoe Zorn CC BY 4.0","mod":"ZFIN","modLink":"https://zfin.org","linkVariable":""}]}},"pageContext":{"id":"abd2d1fd-4308-4401-ad17-d7f589d42d02","citedBy":[],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}