Gene model for the ortholog of Glycogen synthase (GlyS) in the ASM75419v3 Genome Assembly (GenBank AccessionGCA_000754195.3) of Drosophila simulans.
","acknowledgements":"This publication is dedicated to the memory of Dr. James J. Youngblom. We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Cole A. Kiser and Leon F. Laskowski for their help reviewing the model, and Laura K. Reed for overseeing the project. 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":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation"],"email":"mgruysgep@gmail.com","firstName":"Madeline L.","lastName":"Gruys","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3527-2458"},{"affiliations":["The\n University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"masharp2@crimson.ua.edu","firstName":"Madison A.","lastName":"Sharp","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-5590-8599"},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"zrlill@muhlenburg.edu","firstName":"Zachary ","lastName":"Lill","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9444-2672"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"cxiong35@csustan.edu","firstName":"Caroline ","lastName":"Xiong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"hark@muhlenberg.edu","firstName":"Amy T. ","lastName":"Hark","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9782-6452"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"jyoungblom@csustan.edu","firstName":"James J.","lastName":"Youngblom","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-2917-8529"},{"affiliations":["The University of Alabama,\n Tuscaloosa, AL USA"],"departments":[""],"credit":["dataCuration","formalAnalysis","methodology","project","software","supervision","validation","visualization","writing_reviewEditing"],"email":"cprele@ua.edu","firstName":"Chinmay P. ","lastName":"Rele","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"Zip file containing FASTA, PEP, and GFF of the model","doi":null,"resourceType":"Model","name":"DsimGB2_GlyS.zip","url":"https://portal.micropublication.org/uploads/42663d33c28fd15b4d8f3057038f1de0.zip"}],"funding":"This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; 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/6c44359b892df432b8bb5c440e71f88e.png"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for GlyS in Drosophila melanogaster and D. simulans. Thin underlying arrows indicate the DNA strand within which the target gene–GlyS–is located in D. melanogaster (top) and D. simulans (bottom). The thin arrow pointing to the right indicates that GlyS is on the positive (+) strand in D. simulans, and the thin arrow pointing to the left indicates that GlyS is on the negative (-) strand in D. melanogaster. The wide gene arrows pointing in the same direction as GlyS are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of GlyS are on the opposite strand relative to the thin underlying arrows.White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. simulans. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of GlyS in D. simulans are displayed in the User Supplied Track (black); coding exons are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (SRP006203). Splice junctions shown have a read-depth of 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of GlyS-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (y-axis). Amino acid number is indicated along the left and bottom; coding-exon number is indicated along the top and right, and exons are also highlighted with alternating colors. (D) Dot Plot of GlyS-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (y-axis).
","imageTitle":"","methods":"The Genomics Education Partnership maintains a mirror of the UCSC Genome Browser v.435 (Kent WJ et al., 2002; Navarro Gonzalez et al., 2021), which is available at https://gander.wustl.edu. Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2023).
","reagents":"","patternDescription":"Introduction
“Computational gene predictions in non-model organisms often can be improved by careful manual annotation and curation, allowing for more accurate analyses of gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). The Genomics Education Partnership (thegep.org) uses web-based tools to allow undergraduates to participate in course-based research by generating manual annotations of genes in non-model species (Rele et al., 2023). These models of orthologous genes across species, such as the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The particular gene ortholog described here Glycogen synthase (GlyS) in D. simulans was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila.” (Myers et al., 2023) “The IIS pathway is a highly conserved signaling pathway in animals and is central to mediating organismal responses to nutrients (Hietakangas and Cohen 2009; Grewal 2009).” (Myers et al., 2023).
“Glycogen synthase (GlyS; aka. GS) is a gene within the Insulin-signaling pathway in Drosophila and encodes a glycosyltransferase that catalyzes linkage of glucose monomers into glycogen. GlyS activity is regulated allosterically by glucose 6-phosphate and phosphorylation/dephosphorylation allowing for control of cellular glycogen levels (Plyte et al., 1992; Roach et al., 2012). Null GlyS mutants exhibit growth defects and reduced larval viability in Drosophila (Yamada et al., 2019).” (Backlund et al., 2023).
We propose a gene model for the D. simulans ortholog of the D. melanogaster Glycogen synthase (GlyS) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6728025 (RefSeq accession XP_016034640.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3 - Graveley et al., 2011). This model is based on RNA-Seq data from D. simulans (SRP006203) and GlyS in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021).
“D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant 1939; Bock and Wheeler 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster, thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell 1990). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al., 1986) where figs served as a primary host (Lachaise and Tsacas 1983). However, D. simulans's range has expanded worldwide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Lawson et al., 2023).
Synteny
The target gene, GlyS, occurs on chromosome 3R in D. melanogaster and is flanked upstream by Guanylyl cylase at 88E (Gyc88E) and Myofilin (Mf) and downstream by CG3987 and CG3984. The tblastn search of D. melanogaster GlyS-PC (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of GlyS within scaffold CM002913 (CM002913.1) at locus LOC6728025 (XP_016034640.1)— with an E-value of 0.0 and a percent identity of 100.00%. Furthermore, the putative ortholog is flanked upstream by LOC6728023 (XP_016034621.1) and LOC6728024 (XP_044779336.1), which correspond to Gyc88E and Mf in D. melanogaster (E-value: 0.0 and 0.0; identity: 97.27% and 97.82%, respectively, as determined by blastp; Figure 1A, Altschul et al., 1990). The putative ortholog of GlyS is flanked downstream by LOC6728026 (XP_002103378.1) and LOC6728027 (XP_016034642.1), which correspond to CG3987 and CG3984 in D. melanogaster (E-value: 0.0 and 6e-168; identity: 87.14% and 85.13%, respectively, as determined by blastp). The putative ortholog assignment for GlyS in D. simulans is supported by the following evidence: The genes surrounding the GlyS ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by results generated from blastp, so we conclude that LOC6728025 is the correct ortholog of GlyS in D. simulans (Figure 1A).
Protein Model
GlyS in D. simulans has two unique protein-coding isoforms (GlyS-PA and GlyS-PC, identical to GlyS-PB and GlyS-PD; Figure 1B). mRNA isoforms (GlyS-RC, GlyS-RB, GlyS-RD) contain four protein-coding exons and isoform GlyS-RA contains five protein-coding exons. Relative to the ortholog in D. melanogaster, the RNA coding-exon number is conserved. The sequence of GlyS-PC in D. simulans has 100.00% identity (E-value: 0.0) with the protein-coding isoform GlyS-PC in D. melanogaster, as determined by blastp (Figure 1C). The dot plot of the ortholog with GlyS-PA is exhibited in Figure 1D (E-value: 0.0; identity: 100.00%, as determined by blastp. Coordinates of this curated gene model (GlyS-PA, GlyS-PB, GlyS-PC, GlyS-PD) are stored by NCBI at GenBank/BankIt (accession BK064593, BK064594, BK064595, BK064596, respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"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":null},{"reference":"Backlund AE, White J, Grillo L, Ianniello T, Swedrowski A, Yang M, Jemc J, Rele CP, 2023. Gene model for the ortholog of GlyS in Drosophila busckii. microPublication Biology, submitted","pubmedId":null,"doi":null},{"reference":"Bock, I.R., Wheeler, M.R. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428","pubmedId":null,"doi":null},{"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":null},{"reference":"Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al., Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339): 473-9.
","pubmedId":"21179090","doi":null},{"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":null},{"reference":"Koehler A.C., Romo I., Le V., Youngblom J.J., Hark A.T., Rele C.P. 2023. Gene model for the ortholog of GlyS in Drosophila yakuba, microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Lachaise, D., Tsacas, L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 3d: 221--332. FBrf0038884","pubmedId":null,"doi":null},{"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":null},{"reference":"Lawson M.E., Jones G.M., Runion M., Sims D., Young A., Briggs O., Long L.J., Chak S.T.C., Bose I., Rele C.P. 2023. Gene model for the ortholog of ImpL2 in Drosophila simulans. microPublication Biology, submitted","pubmedId":null,"doi":null},{"reference":"Lemeunier, F., David, J., Tsacas, L., Ashburner, M. (1986). The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147--256. FBrf0043749","pubmedId":null,"doi":null},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, et al., Kent WJ. 2021. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 49(D1): D1046-D1057.
","pubmedId":"33221922","doi":null},{"reference":"Powell, Jeffrey R. "Progress and prospects in evolutionary biology: the Drosophila model." (1997).","pubmedId":null,"doi":null},{"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":null},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521
","pubmedId":null,"doi":"10.1101/2020.12.12.420521"},{"reference":"Roach PJ, Depaoli-Roach AA, Hurley TD, Tagliabracci VS. 2012. Glycogen and its metabolism: some new developments and old themes. Biochem J 441(3): 763-87.
","pubmedId":"22248338","doi":null},{"reference":"Plyte SE, Hughes K, Nikolakaki E, Pulverer BJ, Woodgett JR. 1992. Glycogen synthase kinase-3: functions in oncogenesis and development. Biochim Biophys Acta 1114(2-3): 147-62.
","pubmedId":"1333807","doi":null},{"reference":"Grewal SS. 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol 41(5): 1006-10.
","pubmedId":"18992839","doi":null},{"reference":"Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.
","pubmedId":"16577879","doi":null},{"reference":"Sturtevant, A.H., 1919. A new species closely resembling to Drosophila melanogaster. Psyche 26: 488–500. FBrf0000977","pubmedId":null,"doi":null},{"reference":"Yamada T, Habara O, Yoshii Y, Matsushita R, Kubo H, Nojima Y, Nishimura T. 2019. The role of glycogen in development and adult fitness in Drosophila. Development 146(8).
","pubmedId":"30918052","doi":null},{"reference":"Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.
","pubmedId":"19694515","doi":null}],"title":"Gene model for the ortholog of GlyS in Drosophila simulans
","reviews":[],"curatorReviews":[{"curator":{"displayName":"Steven Marygold"},"openAcknowledgement":false,"submitted":"1710237130847"}]},{"id":"ee66be4e-3fb9-4451-b175-f58cc737f26e","decision":"edit","abstract":"Gene model for the ortholog of glycogen synthase (Glys) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"This publication is dedicated to the memory of Dr. James J. Youngblom. We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Cole A. Kiser and Leon F. Laskowski for their help reviewing the model, and Laura K. Reed for overseeing the project. 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":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation"],"email":"mgruysgep@gmail.com","firstName":"Madeline L.","lastName":"Gruys","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3527-2458"},{"affiliations":["The\n University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"masharp2@crimson.ua.edu","firstName":"Madison A.","lastName":"Sharp","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-5590-8599"},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"zrlill@muhlenburg.edu","firstName":"Zachary ","lastName":"Lill","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9444-2672"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"cxiong35@csustan.edu","firstName":"Caroline ","lastName":"Xiong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"hark@muhlenberg.edu","firstName":"Amy T. ","lastName":"Hark","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9782-6452"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"jyoungblom@csustan.edu","firstName":"James J.","lastName":"Youngblom","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-2917-8529"},{"affiliations":["The University of Alabama,\n Tuscaloosa, AL USA"],"departments":[""],"credit":["dataCuration","formalAnalysis","methodology","project","software","supervision","validation","visualization","writing_reviewEditing"],"email":"cprele@ua.edu","firstName":"Chinmay P. ","lastName":"Rele","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[{"awardId":"R25GM130517","funderName":"National Institutes of Health (United States)","awardRecipient":"LK Reed"},{"awardId":"1915544","funderName":"National Science Foundation (United States)","awardRecipient":"LK Reed"}],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"Zip file containing FASTA, PEP, and GFF of the model","doi":null,"resourceType":"Model","name":"DsimGB2_GlyS.zip","url":"https://portal.micropublication.org/uploads/42663d33c28fd15b4d8f3057038f1de0.zip"}],"funding":"This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; 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/6c44359b892df432b8bb5c440e71f88e.png"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for Glys in Drosophila melanogaster and D. simulans. Thin underlying arrows indicate the DNA strand within which the target gene–Glys–is located in D. melanogaster (top) and D. simulans (bottom). The thin arrow pointing to the right indicates that Glys is on the positive (+) strand in D. simulans, and the thin arrow pointing to the left indicates that Glys is on the negative (-) strand in D. melanogaster. The wide gene arrows pointing in the same direction as Glys are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Glys are on the opposite strand relative to the thin underlying arrows.White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. simulans. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Glys in D. simulans are displayed in the User Supplied Track (black); CDSs are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (SRP006203). Splice junctions shown have a read-depth of 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of Glys-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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. (D) Dot Plot of Glys-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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.
","imageTitle":"","methods":"Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2023). Briefly, students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent WJ et al., 2002; Navarro Gonzalez et al., 2021) to examine the genomic neighborhood of their reference IIS gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students then retrieve the protein sequence for the D. melanogaster reference gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly (D. simulans, May 2017 (Princeton ASM75419v2/DsimGB2) - GCA_000754195.3) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify potential orthologs. To validate the potential ortholog, students compare the local genomic neighborhood of their potential ortholog with the genomic neighborhood of their reference gene in D. melanogaster. This local synteny analysis includes at minimum the two upstream and downstream genes relative to their putative ortholog. They also explore other sets of genomic evidence using multiple alignment tracks in the Genome Browser, including BLAT alignments of RefSeq Genes, Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Geneid, Augustus), and modENCODE RNA-Seq from the target species. Genomic structure information (e.g., CDSs, CDS number and boundaries, number of isoforms) for the D. melanogaster reference gene is retrieved through the Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). Approximate splice sites within the target gene are determined using tblastn using the CDSs from the D. melanogaster reference gene. Coordinates of CDSs are then refined by examining aligned modENCODE RNA-Seq data, and by applying paradigms of molecular biology such as identifying canonical splice site sequences and ensuring the maintenance of an open reading frame across hypothesized splice sites. Students then confirm the biological validity of their target gene model using the Gene Model Checker (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023), which compares the structure and translated sequence from their hypothesized target gene model against the D. melanogaster referencegene model. At least two independent models for this gene were generated by students under mentorship of their faculty course instructors. These models were then reconciled by a third independent researcher mentored by the project leaders 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 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 genes in the insulin signaling pathway. \"In this GEP CURE protocol students use web-based tools to manually annotate genes in non-model Drosophila species based on orthology to genes in the well-annotated model organism fruitfly Drosophila melanogaster. The GEP uses web-based tools to allow undergraduates to participate in course-based research by generating manual annotations of genes in non-model species (Rele et al., 2023). Computational-based gene predictions in any organism are often improved by careful manual annotation and curation, allowing for more accurate analyses of gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). These models of orthologous genes across species, such as the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community.” (Myers et al., 2024). “The particular gene ortholog described here was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila. The Insulin/insulin-like growth factor signaling pathway (IIS) is a highly conserved signaling pathway in animals and is central to mediating organismal responses to nutrients (Hietakangas and Cohen 2009; Grewal 2009).” (Myers et al., 2024). “D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant 1939; Bock and Wheeler 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster, thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell 1990). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al., 1986) where figs served as a primary host (Lachaise and Tsacas 1983). However, D. simulans's range has expanded worldwide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Lawson et al., 2024). “Glycogen synthase (Glys; aka. GS, GlyS) is a gene within the Insulin-signaling pathway in Drosophila and encodes a glycosyltransferase that catalyzes linkage of glucose monomers into glycogen. Glys activity is regulated allosterically by glucose 6-phosphate and phosphorylation/dephosphorylation allowing for control of cellular glycogen levels (Plyte et al., 1992; Roach et al., 2012). Null Glys mutants exhibit growth defects and reduced larval viability in Drosophila (Yamada et al., 2019).” (Backlund et al., 2024). |
We propose a gene model for the D. simulans ortholog of the D. melanogaster Glycogen synthase (Glys) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6728025 (RefSeq accession XP_016034640.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3). This model is based on RNA-Seq data from D. simulans (SRP006203 - Graveley et al., 2011) and Glys in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021). Gene and species details can be found in the description above.
Synteny
The reference gene, Glys, occurs on chromosome 3R in D. melanogaster and is flanked upstream by Guanylyl cylase at 88E (Gyc88E) and Myofilin (Mf) and downstream by CG3987 and CG3984. The tblastn search of D. melanogaster Glys-PC (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of Glys within scaffold CM002913 (CM002913.1) at locus LOC6728025 (XP_016034640.1)— with an E-value of 0.0 and a percent identity of 100.00%. Furthermore, the putative ortholog is flanked upstream by LOC6728023 (XP_016034621.1) and LOC6728024 (XP_044779336.1), which correspond to Gyc88E and Mf in D. melanogaster (E-value: 0.0 and 0.0; identity: 97.27% and 97.82%, respectively, as determined by blastp; Figure 1A, Altschul et al., 1990). The putative ortholog of Glys is flanked downstream by LOC6728026 (XP_002103378.1) and LOC6728027 (XP_016034642.1), which correspond to CG3987 and CG3984 in D. melanogaster (E-value: 0.0 and 6e-168; identity: 87.14% and 85.13%, respectively, as determined by blastp). The putative ortholog assignment for Glys in D. simulans is supported by the following evidence: The genes surrounding the Glys ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by results generated from blastp, so we conclude that LOC6728025 is the correct ortholog of Glys in D. simulans (Figure 1A).
Protein Model
Glys in D. simulans has two unique protein-coding isoforms (Glys-PA and Glys-PC, identical to Glys-PB and Glys-PD; Figure 1B). mRNA isoforms Glys-RC, Glys-RB, and Glys-RD, which differ in their UTRs, contain four protein-coding CDSs ,and isoform Glys-RA contains five protein-coding CDSs. Relative to the ortholog in D. melanogaster, the RNA CDS number is conserved. The sequence of Glys-PC in D. simulans has 100.00% identity (E-value: 0.0) with the protein-coding isoform Glys-PC in D. melanogaster, as determined by blastp (Figure 1C). The dot plot of the ortholog with Glys-PA is exhibited in Figure 1D (E-value: 0.0; identity: 100.00%, as determined by blastp. Coordinates of this curated gene model (Glys-PA, Glys-PB, Glys-PC, Glys-PD) are stored by NCBI at GenBank/BankIt (accession BK064593, BK064594, BK064595, BK064596, respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"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":null},{"reference":"Backlund AE, White J, Grillo L, Ianniello T, Swedrowski A, Yang M, Jemc J, Rele CP, 2024. Gene model for the ortholog of GlyS in Drosophila busckii. microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Bock, I.R., Wheeler, M.R. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428","pubmedId":null,"doi":null},{"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":null},{"reference":"Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al., Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339): 473-9.
","pubmedId":"21179090","doi":null},{"reference":"Grewal SS. 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol 41(5): 1006-10.
","pubmedId":"18992839","doi":null},{"reference":"Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.
","pubmedId":"19694515","doi":null},{"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":null},{"reference":"Koehler A.C., Romo I., Le V., Youngblom J.J., Hark A.T., Rele C.P. 2023. Gene model for the ortholog of GlyS in Drosophila yakuba, microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Lachaise, D., Tsacas, L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 3d: 221--332. FBrf0038884","pubmedId":null,"doi":null},{"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":null},{"reference":"Lawson M.E., Jones G.M., Runion M., Sims D., Young A., Briggs O., Long L.J., Chak S.T.C., Bose I., Rele C.P. 2024. Gene model for the ortholog of ImpL2 in Drosophila simulans. microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Lemeunier, F., David, J., Tsacas, L., Ashburner, M. (1986). The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147--256. FBrf0043749","pubmedId":null,"doi":null},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, et al., Kent WJ. 2021. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 49(D1): D1046-D1057.
","pubmedId":"33221922","doi":null},{"reference":"Plyte SE, Hughes K, Nikolakaki E, Pulverer BJ, Woodgett JR. 1992. Glycogen synthase kinase-3: functions in oncogenesis and development. Biochim Biophys Acta 1114(2-3): 147-62.
","pubmedId":"1333807","doi":null},{"reference":"Powell, Jeffrey R. "Progress and prospects in evolutionary biology: the Drosophila model." (1997).","pubmedId":null,"doi":null},{"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":null},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521
","pubmedId":null,"doi":"10.1101/2020.12.12.420521"},{"reference":"Roach PJ, Depaoli-Roach AA, Hurley TD, Tagliabracci VS. 2012. Glycogen and its metabolism: some new developments and old themes. Biochem J 441(3): 763-87.
","pubmedId":"22248338","doi":null},{"reference":"Sturtevant, A.H., 1919. A new species closely resembling to Drosophila melanogaster. Psyche 26: 488–500. FBrf0000977","pubmedId":null,"doi":null},{"reference":"Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.
","pubmedId":"16577879","doi":null},{"reference":"Yamada T, Habara O, Yoshii Y, Matsushita R, Kubo H, Nojima Y, Nishimura T. 2019. The role of glycogen in development and adult fitness in Drosophila. Development 146(8).
","pubmedId":"30918052","doi":null}],"title":"Gene model for the ortholog of Glys in Drosophila simulans
","reviews":[{"reviewer":{"displayName":"Shan Hays"},"openAcknowledgement":false,"status":{"submitted":true}},{"reviewer":{"displayName":"Thomas Giarla"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"Steven Marygold"},"openAcknowledgement":false,"submitted":null}]},{"id":"e9198ed2-2946-44c5-8482-565b928c86c3","decision":"accept","abstract":"Gene model for the ortholog of glycogen synthase (Glys) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"This publication is dedicated to the memory of Dr. James J. Youngblom. We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Cole A. Kiser and Leon F. Laskowski for their help reviewing the model, and Laura K. Reed for overseeing the project. 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":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation"],"email":"mgruysgep@gmail.com","firstName":"Madeline L.","lastName":"Gruys","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3527-2458"},{"affiliations":["The\n University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"masharp2@crimson.ua.edu","firstName":"Madison A.","lastName":"Sharp","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-5590-8599"},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"zrlill@muhlenburg.edu","firstName":"Zachary ","lastName":"Lill","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9444-2672"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"cxiong35@csustan.edu","firstName":"Caroline ","lastName":"Xiong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"hark@muhlenberg.edu","firstName":"Amy T. ","lastName":"Hark","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9782-6452"},{"affiliations":["California State University\n Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"jyoungblom@csustan.edu","firstName":"James J.","lastName":"Youngblom","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-2917-8529"},{"affiliations":["The University of Alabama,\n Tuscaloosa, AL USA"],"departments":[""],"credit":["dataCuration","formalAnalysis","methodology","project","software","supervision","validation","visualization","writing_reviewEditing"],"email":"gep@ua.edu","firstName":"Chinmay P. ","lastName":"Rele","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[{"awardId":"R25GM130517","funderName":"National Institutes of Health (United States)","awardRecipient":"LK Reed"},{"awardId":"1915544","funderName":"National Science Foundation (United States)","awardRecipient":"LK Reed"}],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"Zip file containing FASTA, PEP, and GFF of the model","doi":"10.22002/mkhd1-mtk87","resourceType":"Model","name":"DsimGB2_GlyS.zip","url":"https://portal.micropublication.org/uploads/42663d33c28fd15b4d8f3057038f1de0.zip"}],"funding":"This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; 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/6c44359b892df432b8bb5c440e71f88e.png"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for Glys in Drosophila melanogaster and D. simulans. Thin underlying arrows indicate the DNA strand within which the target gene–Glys–is located in D. melanogaster (top) and D. simulans (bottom). The thin arrow pointing to the right indicates that Glys is on the positive (+) strand in D. simulans, and the thin arrow pointing to the left indicates that Glys is on the negative (-) strand in D. melanogaster. The wide gene arrows pointing in the same direction as Glys are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Glys are on the opposite strand relative to the thin underlying arrows.White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. simulans. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Glys in D. simulans are displayed in the User Supplied Track (black); CDSs are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (SRP006203). Splice junctions shown have a read-depth of 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of Glys-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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. (D) Dot Plot of Glys-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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.
","imageTitle":"Glys gene model comparison between Drosophila simulans and Drosophila melanogaster orthologs
","methods":"Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2023). Briefly, students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent WJ et al., 2002; Navarro Gonzalez et al., 2021) to examine the genomic neighborhood of their reference IIS gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students then retrieve the protein sequence for the D. melanogaster reference gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly (D. simulans, May 2017 (Princeton ASM75419v2/DsimGB2) - GCA_000754195.3) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify potential orthologs. To validate the potential ortholog, students compare the local genomic neighborhood of their potential ortholog with the genomic neighborhood of their reference gene in D. melanogaster. This local synteny analysis includes at minimum the two upstream and downstream genes relative to their putative ortholog. They also explore other sets of genomic evidence using multiple alignment tracks in the Genome Browser, including BLAT alignments of RefSeq Genes, Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Geneid, Augustus), and modENCODE RNA-Seq from the target species. Genomic structure information (e.g., CDSs, CDS number and boundaries, number of isoforms) for the D. melanogaster reference gene is retrieved through the Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). Approximate splice sites within the target gene are determined using tblastn using the CDSs from the D. melanogaster reference gene. Coordinates of CDSs are then refined by examining aligned modENCODE RNA-Seq data, and by applying paradigms of molecular biology such as identifying canonical splice site sequences and ensuring the maintenance of an open reading frame across hypothesized splice sites. Students then confirm the biological validity of their target gene model using the Gene Model Checker (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023), which compares the structure and translated sequence from their hypothesized target gene model against the D. melanogaster referencegene model. At least two independent models for this gene were generated by students under mentorship of their faculty course instructors. These models were then reconciled by a third independent researcher mentored by the project leaders 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 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 genes in the insulin signaling pathway. \"In this GEP CURE protocol students use web-based tools to manually annotate genes in non-model Drosophila species based on orthology to genes in the well-annotated model organism fruitfly Drosophila melanogaster. The GEP uses web-based tools to allow undergraduates to participate in course-based research by generating manual annotations of genes in non-model species (Rele et al., 2023). Computational-based gene predictions in any organism are often improved by careful manual annotation and curation, allowing for more accurate analyses of gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). These models of orthologous genes across species, such as the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community.” (Myers et al., 2024). “The particular gene ortholog described here was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila. The Insulin/insulin-like growth factor signaling pathway (IIS) is a highly conserved signaling pathway in animals and is central to mediating organismal responses to nutrients (Hietakangas and Cohen 2009; Grewal 2009).” (Myers et al., 2024). “D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant 1939; Bock and Wheeler 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster, thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell 1990). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al., 1986) where figs served as a primary host (Lachaise and Tsacas 1983). However, D. simulans's range has expanded worldwide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Lawson et al., 2024). “Glycogen synthase (Glys; aka. GS, GlyS) is a gene within the Insulin-signaling pathway in Drosophila and encodes a glycosyltransferase that catalyzes linkage of glucose monomers into glycogen. Glys activity is regulated allosterically by glucose 6-phosphate and phosphorylation/dephosphorylation allowing for control of cellular glycogen levels (Plyte et al., 1992; Roach et al., 2012). Null Glys mutants exhibit growth defects and reduced larval viability in Drosophila (Yamada et al., 2019).” (Backlund et al., 2024). |
We propose a gene model for the D. simulans ortholog of the D. melanogaster Glycogen synthase (Glys) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6728025 (RefSeq accession XP_016034640.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3). This model is based on RNA-Seq data from D. simulans (SRP006203 - Graveley et al., 2011) and Glys in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021). Gene and species details can be found in the description above.
Synteny
The reference gene, Glys, occurs on chromosome 3R in D. melanogaster and is flanked upstream by Guanylyl cylase at 88E (Gyc88E) and Myofilin (Mf) and downstream by CG3987 and CG3984. The tblastn search of D. melanogaster Glys-PC (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of Glys within scaffold CM002913 (CM002913.1) at locus LOC6728025 (XP_016034640.1)— with an E-value of 0.0 and a percent identity of 100.00%. Furthermore, the putative ortholog is flanked upstream by LOC6728023 (XP_016034621.1) and LOC6728024 (XP_044779336.1), which correspond to Gyc88E and Mf in D. melanogaster (E-value: 0.0 and 0.0; identity: 97.27% and 97.82%, respectively, as determined by blastp; Figure 1A, Altschul et al., 1990). The putative ortholog of Glys is flanked downstream by LOC6728026 (XP_002103378.1) and LOC6728027 (XP_016034642.1), which correspond to CG3987 and CG3984 in D. melanogaster (E-value: 0.0 and 6e-168; identity: 87.14% and 85.13%, respectively, as determined by blastp). The putative ortholog assignment for Glys in D. simulans is supported by the following evidence: The genes surrounding the Glys ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by results generated from blastp, so we conclude that LOC6728025 is the correct ortholog of Glys in D. simulans (Figure 1A).
Protein Model
Glys in D. simulans has two unique protein-coding isoforms (Glys-PA and Glys-PC, identical to Glys-PB and Glys-PD; Figure 1B). mRNA isoforms Glys-RC, Glys-RB, and Glys-RD, which differ in their UTRs, contain four protein-coding CDSs ,and isoform Glys-RA contains five protein-coding CDSs. Relative to the ortholog in D. melanogaster, the RNA CDS number is conserved. The sequence of Glys-PC in D. simulans has 100.00% identity (E-value: 0.0) with the protein-coding isoform Glys-PC in D. melanogaster, as determined by blastp (Figure 1C). The dot plot of the ortholog with Glys-PA is exhibited in Figure 1D (E-value: 0.0; identity: 100.00%, as determined by blastp. Coordinates of this curated gene model (Glys-PA, Glys-PB, Glys-PC, Glys-PD) are stored by NCBI at GenBank/BankIt (accession BK064593, BK064594, BK064595, BK064596, respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"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":null},{"reference":"Backlund AE, White J, Grillo L, Ianniello T, Swedrowski A, Yang M, Jemc J, Rele CP, 2024. Gene model for the ortholog of Glys in Drosophila busckii. microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Bock IR, Wheeler MR. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1-102. FBrf0024428
","pubmedId":null,"doi":null},{"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":null},{"reference":"Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al., Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339): 473-9.
","pubmedId":"21179090","doi":null},{"reference":"Grewal SS. 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol 41(5): 1006-10.
","pubmedId":"18992839","doi":null},{"reference":"Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.
","pubmedId":"19694515","doi":null},{"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":null},{"reference":"Koehler AC, Romo I, Le V, Youngblom JJ, Hark AT, Rele CP, Reed LK. 2024. Gene model for the ortholog of Glys in Drosophila yakuba. MicroPubl Biol 2024.
","pubmedId":null,"doi":"10.17912/micropub.biology.000983"},{"reference":"Lachaise D, Tsacas L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 3d: 221-332. FBrf0038884
","pubmedId":null,"doi":null},{"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":null},{"reference":"Lawson ME, Jones GM, Runion M, Sims D, Young A, Briggs O, et al., Reed LK. 2024. Gene model for the ortholog of ImpL2 in Drosophila simulans. MicroPubl Biol 2024.
","pubmedId":"39677518","doi":null},{"reference":"Lemeunier F, David J, Tsacas L, Ashburner M. (1986). The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147-256. FBrf0043749
","pubmedId":null,"doi":null},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, et al., Kent WJ. 2021. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 49(D1): D1046-D1057.
","pubmedId":"33221922","doi":null},{"reference":"Plyte SE, Hughes K, Nikolakaki E, Pulverer BJ, Woodgett JR. 1992. Glycogen synthase kinase-3: functions in oncogenesis and development. Biochim Biophys Acta 1114(2-3): 147-62.
","pubmedId":"1333807","doi":null},{"reference":"Powell JR. \"Progress and prospects in evolutionary biology: the Drosophila model.\" (1997).
","pubmedId":null,"doi":null},{"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":null},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521
","pubmedId":null,"doi":"10.1101/2020.12.12.420521"},{"reference":"Roach PJ, Depaoli-Roach AA, Hurley TD, Tagliabracci VS. 2012. Glycogen and its metabolism: some new developments and old themes. Biochem J 441(3): 763-87.
","pubmedId":"22248338","doi":null},{"reference":"Sturtevant AH, 1919. A new species closely resembling Drosophila melanogaster. Psyche 26: 488-500. FBrf0000977
","pubmedId":null,"doi":null},{"reference":"Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.
","pubmedId":"16577879","doi":null},{"reference":"Yamada T, Habara O, Yoshii Y, Matsushita R, Kubo H, Nojima Y, Nishimura T. 2019. The role of glycogen in development and adult fitness in Drosophila. Development 146(8).
","pubmedId":"30918052","doi":null}],"title":"Gene model for the ortholog of Glys in Drosophila simulans
","reviews":[],"curatorReviews":[{"curator":{"displayName":"Steven Marygold"},"openAcknowledgement":false,"submitted":null}]},{"id":"aed6f88f-9d01-43b3-8ba8-ba8b9bc8d34b","decision":"edit","abstract":"Gene model for the ortholog of glycogen synthase (Glys) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"This publication is dedicated to the memory of Dr. James J. Youngblom. We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Cole A. Kiser and Leon F. Laskowski for their help reviewing the model. 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":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation"],"email":"mgruysgep@gmail.com","firstName":"Madeline L.","lastName":"Gruys","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3527-2458"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"masharp2@crimson.ua.edu","firstName":"Madison A.","lastName":"Sharp","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-5590-8599"},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"zrlill@muhlenburg.edu","firstName":"Zachary ","lastName":"Lill","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9444-2672"},{"affiliations":["California State University Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"cxiong35@csustan.edu","firstName":"Caroline ","lastName":"Xiong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["Muhlenburg College, Allentown, PA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"hark@muhlenberg.edu","firstName":"Amy T. ","lastName":"Hark","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9782-6452"},{"affiliations":["California State University Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"jyoungblom@csustan.edu","firstName":"James J.","lastName":"Youngblom","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-2917-8529"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["dataCuration","formalAnalysis","methodology","project","software","supervision","validation","visualization","writing_reviewEditing"],"email":"gep@ua.edu","firstName":"Chinmay P. ","lastName":"Rele","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["supervision","fundingAcquisition","conceptualization","project","writing_reviewEditing"],"email":"lreed1@ua.edu","firstName":"Laura K","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":null,"WBId":"","orcid":"0000-0002-4381-494X"}],"awards":[{"awardId":"R25GM130517","funderName":"National Institutes of Health (United States)","awardRecipient":"LK Reed"},{"awardId":"1915544","funderName":"National Science Foundation (United States)","awardRecipient":"LK Reed"}],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"File contains the GFF, aminio acid, and nucleic acid sequences for the gene model.","doi":"10.22002/ywzts-78198","resourceType":"Model","name":"DsimGB2_Glys.zip","url":"https://portal.micropublication.org/uploads/92ae8dabcfb65bc49fd495c883548abe.zip"}],"funding":"This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; 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/6c44359b892df432b8bb5c440e71f88e.png"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for Glys in Drosophila melanogaster and D. simulans. Thin underlying arrows indicate the DNA strand within which the target gene–Glys–is located in D. melanogaster (top) and D. simulans (bottom) genomes. The thin arrow pointing to the right indicates that Glys is on the positive (+) strand in D. simulans, and the thin arrow pointing to the left indicates that Glys is on the negative (-) strand in D. melanogaster. The wide gene arrows pointing in the same direction as Glys are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Glys are on the opposite strand relative to the thin underlying arrows.White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. simulans. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Glys in D. simulans are displayed in the User Supplied Track (black); CDSs are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (SRP006203). Splice junctions shown have a read-depth of 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of Glys-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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. (D) Dot Plot of Glys-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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.
","imageTitle":"Glys gene model comparison between Drosophila simulans and Drosophila melanogaster orthologs
","methods":"Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2023). Briefly, students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent WJ et al., 2002; Navarro Gonzalez et al., 2021) to examine the genomic neighborhood of their reference IIS gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students then retrieve the protein sequence for the D. melanogaster reference gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi; Altschul et al., 1990) to identify potential orthologs. To validate the potential ortholog, students compare the local genomic neighborhood of their potential ortholog with the genomic neighborhood of their reference gene in D. melanogaster. This local synteny analysis includes at minimum the two upstream and downstream genes relative to their putative ortholog. They also explore other sets of genomic evidence using multiple alignment tracks in the Genome Browser, including BLAT alignments of RefSeq Genes, Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Geneid, Augustus), and modENCODE RNA-Seq from the target species. Detailed explanation of how these lines of genomic evidenced are leveraged by students in gene model development are described in Rele et al. (2023). Genomic structure information (e.g., CDSs, intron-exon number and boundaries, number of isoforms) for the D. melanogaster reference gene is retrieved through the Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). Approximate splice sites within the target gene are determined using tblastn using the CDSs from the D. melanogaster reference gene. Coordinates of CDSs are then refined by examining aligned modENCODE RNA-Seq data, and by applying paradigms of molecular biology such as identifying canonical splice site sequences and ensuring the maintenance of an open reading frame across hypothesized splice sites. Students then confirm the biological validity of their target gene model using the Gene Model Checker (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023), which compares the structure and translated sequence from their hypothesized target gene model against the D. melanogaster reference gene model. At least two independent models for a gene are generated by students under mentorship of their faculty course instructors. Those models are then reconciled by a third independent researcher mentored by the project leaders to produce the final model. 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 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 genes in the insulin signaling pathway. \"In this GEP CURE protocol students use web-based tools to manually annotate genes in non-model Drosophila species based on orthology to genes in the well-annotated model organism fruitfly Drosophila melanogaster. The GEP uses web-based tools to allow undergraduates to participate in course-based research by generating manual annotations of genes in non-model species (Rele et al., 2023). Computational-based gene predictions in any organism are often improved by careful manual annotation and curation, allowing for more accurate analyses of gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). These models of orthologous genes across species, such as the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community.” (Myers et al., 2024). “The particular gene ortholog described here was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila. The Insulin/insulin-like growth factor signaling pathway (IIS) is a highly conserved signaling pathway in animals and is central to mediating organismal responses to nutrients (Hietakangas and Cohen 2009; Grewal 2009).” (Myers et al., 2024). “D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant 1939; Bock and Wheeler 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster, thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell 1997). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al., 1986) where figs served as a primary host (Lachaise and Tsacas 1983). However, D. simulans's range has expanded worldwide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Lawson et al., 2024). “Glycogen synthase (Glys; aka. GS, GlyS) is a gene within the Insulin-signaling pathway in Drosophila and encodes a glycosyltransferase that catalyzes linkage of glucose monomers into glycogen. Glys activity is regulated allosterically by glucose 6-phosphate and phosphorylation/dephosphorylation allowing for control of cellular glycogen levels (Plyte et al., 1992; Roach et al., 2012). Null Glys mutants exhibit growth defects and reduced larval viability in Drosophila (Yamada et al., 2019).” (Backlund et al., 2024). |
We propose a gene model for the D. simulans ortholog of the D. melanogaster Glycogen synthase (Glys) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6728025 (RefSeq accession XP_016034640.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3 - Hu et al., 2013). This model is based on RNA-Seq data from D. simulans (SRP006203 - Graveley et al., 2011) and Glys in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021). Gene and species details can be found in the description above.
Synteny
The reference gene, Glys, occurs on chromosome 3R in D. melanogaster and is flanked upstream by Guanylyl cylase at 88E (Gyc88E) and Myofilin (Mf) and downstream by CG3987 and CG3984. The tblastn search of D. melanogaster Glys-PC (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of Glys within scaffold CM002913 (CM002913.1) at locus LOC6728025 (XP_016034640.1)— with an E-value of 0.0 and a percent identity of 100.00%. Furthermore, the putative ortholog is flanked upstream by LOC6728023 (XP_016034621.1) and LOC6728024 (XP_044779336.1), which correspond to Gyc88E and Mf in D. melanogaster (E-value: 0.0 and 0.0; identity: 97.27% and 97.82%, respectively, as determined by blastp; Figure 1A, Altschul et al., 1990). The putative ortholog of Glys is flanked downstream by LOC6728026 (XP_002103378.1) and LOC6728027 (XP_016034642.1), which correspond to CG3987 and CG3984 in D. melanogaster (E-value: 0.0 and 6e-168; identity: 87.14% and 85.13%, respectively, as determined by blastp). The putative ortholog assignment for Glys in D. simulans is supported by the following evidence: The genes surrounding the Glys ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by results generated from blastp, so we conclude that LOC6728025 is the correct ortholog of Glys in D. simulans (Figure 1A).
Protein Model
Glys in D. simulans has two unique protein-coding isoforms (Glys-PA and Glys-PC, identical to Glys-PB and Glys-PD; Figure 1B). mRNA isoforms Glys-RC, Glys-RB, and Glys-RD, which differ in their UTRs, contain four CDSs ,and isoform Glys-RA contains five CDSs. Relative to the ortholog in D. melanogaster, the RNA CDS number is conserved. The sequence of Glys-PC in D. simulans has 100.00% identity (E-value: 0.0) with the protein-coding isoform Glys-PC in D. melanogaster, as determined by blastp (Figure 1C). The dot plot of the ortholog with Glys-PA is exhibited in Figure 1D (E-value: 0.0; identity: 100.00%, as determined by blastp. Coordinates of this curated gene model (Glys-PA, Glys-PB, Glys-PC, Glys-PD) are stored by NCBI at GenBank/BankIt (accession BK064593, BK064594, BK064595, BK064596, respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"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":null},{"reference":"Backlund AE, White J, Grillo L, Ianniello T, Swedrowski A, Yang M, Jemc J, Rele CP, 2024. Gene model for the ortholog of Glys in Drosophila busckii. microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Bock IR., Wheeler MR. 1972. The Drosophila melanogaster species-group. The University of Texas Publication. 7213: 1-102. FBrf0024428.
","pubmedId":null,"doi":null},{"reference":"Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al., Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339): 473-9.
","pubmedId":"21179090","doi":null},{"reference":"Grewal SS. 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol 41(5): 1006-10.
","pubmedId":"18992839","doi":null},{"reference":"Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.
","pubmedId":"19694515","doi":null},{"reference":"Hu TT, Eisen MB, Thornton KR, Andolfatto P. 2013. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 23(1): 89-98.
","pubmedId":"22936249","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":null},{"reference":"Koehler AC, Romo I, Le V, Youngblom JJ, Hark AT, Rele CP, Reed LK. 2024. Gene model for the ortholog of Glys in Drosophila yakuba. MicroPubl Biol 2024.
","pubmedId":null,"doi":"10.17912/micropub.biology.000983"},{"reference":"Lachaise D, Tsacas L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 3d: 221-332. FBrf0038884
","pubmedId":null,"doi":null},{"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":null},{"reference":"Lawson ME, Jones GM, Runion M, Sims D, Young A, Briggs O, et al., Reed LK. 2024. Gene model for the ortholog of ImpL2 in Drosophila simulans. MicroPubl Biol 2024.
","pubmedId":"39677518","doi":null},{"reference":"Lemeunier F, David J, Tsacas L, Ashburner M. 1986. The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147-256. FBrf0043749
","pubmedId":null,"doi":null},{"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":"Myers A, Hoffman A, Natysin M, Arsham AM, Stamm J, Thompson JS, Rele CP, Reed LK. 2024. Gene model for the ortholog Myc in Drosophila ananassae. MicroPubl Biol 2024.
","pubmedId":"39677519","doi":"10.17912/micropub.biology.000856"},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, et al., Kent WJ. 2021. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 49(D1): D1046-D1057.
","pubmedId":"33221922","doi":null},{"reference":"Plyte SE, Hughes K, Nikolakaki E, Pulverer BJ, Woodgett JR. 1992. Glycogen synthase kinase-3: functions in oncogenesis and development. Biochim Biophys Acta 1114(2-3): 147-62.
","pubmedId":"1333807","doi":null},{"reference":"Powell JR. 1997. Progress and prospects in evolutionary biology: the Drosophila model. Oxford University Press, ISBN: 9780195076912
","pubmedId":null,"doi":null},{"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":null},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521
","pubmedId":null,"doi":"10.1101/2020.12.12.420521"},{"reference":"Roach PJ, Depaoli-Roach AA, Hurley TD, Tagliabracci VS. 2012. Glycogen and its metabolism: some new developments and old themes. Biochem J 441(3): 763-87.
","pubmedId":"22248338","doi":null},{"reference":"Sturtevant AH, 1919. A new species closely resembling Drosophila melanogaster. Psyche 26: 488-500. FBrf0000977
","pubmedId":null,"doi":null},{"reference":"Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.
","pubmedId":"16577879","doi":null},{"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":"Yamada T, Habara O, Yoshii Y, Matsushita R, Kubo H, Nojima Y, Nishimura T. 2019. The role of glycogen in development and adult fitness in Drosophila. Development 146(8).
","pubmedId":"30918052","doi":null}],"title":"Gene model for the ortholog of Glys in Drosophila simulans
","reviews":[],"curatorReviews":[{"curator":{"displayName":"Steven Marygold"},"openAcknowledgement":false,"submitted":null}]},{"id":"ca0091b9-c671-41b7-bf12-ea6c791eeaaa","decision":"publish","abstract":"Gene model for the ortholog of glycogen synthase (Glys) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.
","acknowledgements":"This publication is dedicated to the memory of Dr. James J. Youngblom. We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Cole A. Kiser and Leon F. Laskowski for their help reviewing the model. 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":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation"],"email":"mgruysgep@gmail.com","firstName":"Madeline L.","lastName":"Gruys","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3527-2458"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"masharp2@crimson.ua.edu","firstName":"Madison A.","lastName":"Sharp","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-5590-8599"},{"affiliations":["Muhlenburg College, Allentown,\n PA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"zrlill@muhlenburg.edu","firstName":"Zachary ","lastName":"Lill","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9444-2672"},{"affiliations":["California State University Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"cxiong35@csustan.edu","firstName":"Caroline ","lastName":"Xiong","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["Muhlenburg College, Allentown, PA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"hark@muhlenberg.edu","firstName":"Amy T. ","lastName":"Hark","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-9782-6452"},{"affiliations":["California State University Stanislaus, Turlock, CA USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"jyoungblom@csustan.edu","firstName":"James J.","lastName":"Youngblom","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-2917-8529"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["dataCuration","formalAnalysis","methodology","project","software","supervision","validation","visualization","writing_reviewEditing"],"email":"cprele@ua.edu","firstName":"Chinmay P. ","lastName":"Rele","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["supervision","fundingAcquisition","conceptualization","project","writing_reviewEditing"],"email":"lreed1@ua.edu","firstName":"Laura K","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":null,"WBId":"","orcid":"0000-0002-4381-494X"}],"awards":[{"awardId":"R25GM130517","funderName":"National Institutes of Health (United States)","awardRecipient":"LK Reed"},{"awardId":"1915544","funderName":"National Science Foundation (United States)","awardRecipient":"LK Reed"}],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"File contains the GFF, aminio acid, and nucleic acid sequences for the gene model.","doi":"10.22002/ywzts-78198","resourceType":"Model","name":"DsimGB2_Glys.zip","url":"https://portal.micropublication.org/uploads/92ae8dabcfb65bc49fd495c883548abe.zip"}],"funding":"This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; 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/6c44359b892df432b8bb5c440e71f88e.png"},"imageCaption":"(A) Synteny comparison of the genomic neighborhoods for Glys in Drosophila melanogaster and D. simulans. Thin underlying arrows indicate the DNA strand within which the target gene–Glys–is located in D. melanogaster (top) and D. simulans (bottom) genomes. The thin arrow pointing to the right indicates that Glys is on the positive (+) strand in D. simulans, and the thin arrow pointing to the left indicates that Glys is on the negative (-) strand in D. melanogaster. The wide gene arrows pointing in the same direction as Glys are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Glys are on the opposite strand relative to the thin underlying arrows.White gene arrows in D. simulans indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. simulans gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. simulans. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Glys in D. simulans are displayed in the User Supplied Track (black); CDSs are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. simulans), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. simulans), and Splice Junctions Predicted by regtools using D. simulans RNA-Seq (SRP006203). Splice junctions shown have a read-depth of 10-49, 50-99, 100-499, 500-999, >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of Glys-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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. (D) Dot Plot of Glys-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. simulans (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.
","imageTitle":"Glys gene model comparison between Drosophila simulans and Drosophila melanogaster orthologs
","methods":"Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2023). Briefly, students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu; Kent WJ et al., 2002; Navarro Gonzalez et al., 2021) to examine the genomic neighborhood of their reference IIS gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students then retrieve the protein sequence for the D. melanogaster reference gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi; Altschul et al., 1990) to identify potential orthologs. To validate the potential ortholog, students compare the local genomic neighborhood of their potential ortholog with the genomic neighborhood of their reference gene in D. melanogaster. This local synteny analysis includes at minimum the two upstream and downstream genes relative to their putative ortholog. They also explore other sets of genomic evidence using multiple alignment tracks in the Genome Browser, including BLAT alignments of RefSeq Genes, Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Geneid, Augustus), and modENCODE RNA-Seq from the target species. Detailed explanation of how these lines of genomic evidenced are leveraged by students in gene model development are described in Rele et al. (2023). Genomic structure information (e.g., CDSs, intron-exon number and boundaries, number of isoforms) for the D. melanogaster reference gene is retrieved through the Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023). Approximate splice sites within the target gene are determined using tblastn using the CDSs from the D. melanogaster reference gene. Coordinates of CDSs are then refined by examining aligned modENCODE RNA-Seq data, and by applying paradigms of molecular biology such as identifying canonical splice site sequences and ensuring the maintenance of an open reading frame across hypothesized splice sites. Students then confirm the biological validity of their target gene model using the Gene Model Checker (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al., 2023), which compares the structure and translated sequence from their hypothesized target gene model against the D. melanogaster reference gene model. At least two independent models for a gene are generated by students under mentorship of their faculty course instructors. Those models are then reconciled by a third independent researcher mentored by the project leaders to produce the final model. 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 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 genes in the insulin signaling pathway. \"In this GEP CURE protocol students use web-based tools to manually annotate genes in non-model Drosophila species based on orthology to genes in the well-annotated model organism fruitfly Drosophila melanogaster. The GEP uses web-based tools to allow undergraduates to participate in course-based research by generating manual annotations of genes in non-model species (Rele et al., 2023). Computational-based gene predictions in any organism are often improved by careful manual annotation and curation, allowing for more accurate analyses of gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). These models of orthologous genes across species, such as the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community.” (Myers et al., 2024). “The particular gene ortholog described here was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila. The Insulin/insulin-like growth factor signaling pathway (IIS) is a highly conserved signaling pathway in animals and is central to mediating organismal responses to nutrients (Hietakangas and Cohen 2009; Grewal 2009).” (Myers et al., 2024). “D. simulans is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila (Sturtevant 1939; Bock and Wheeler 1972). It was first described by Sturtevant (1919). D. simulans is a sibling species to D. melanogaster, thus extensively studied in the context of speciation genetics and evolutionary ecology (Powell 1997). Historically, D. simulans was a tropical species native to sub-Saharan Africa (Lemeunier et al., 1986) where figs served as a primary host (Lachaise and Tsacas 1983). However, D. simulans's range has expanded worldwide within the last century as a human commensal using a broad range of rotting fruits as breeding sites (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Lawson et al., 2024). “Glycogen synthase (Glys; aka. GS, GlyS) is a gene within the Insulin-signaling pathway in Drosophila and encodes a glycosyltransferase that catalyzes linkage of glucose monomers into glycogen. Glys activity is regulated allosterically by glucose 6-phosphate and phosphorylation/dephosphorylation allowing for control of cellular glycogen levels (Plyte et al., 1992; Roach et al., 2012). Null Glys mutants exhibit growth defects and reduced larval viability in Drosophila (Yamada et al., 2019).” (Backlund et al., 2024). |
We propose a gene model for the D. simulans ortholog of the D. melanogaster Glycogen synthase (Glys) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC6728025 (RefSeq accession XP_016034640.1) in the ASM75419v3 Genome Assembly of D. simulans (GenBank Accession: GCA_000754195.3 - Hu et al., 2013). This model is based on RNA-Seq data from D. simulans (SRP006203 - Graveley et al., 2011) and Glys in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021). Gene and species details can be found in the description above.
Synteny
The reference gene, Glys, occurs on chromosome 3R in D. melanogaster and is flanked upstream by Guanylyl cylase at 88E (Gyc88E) and Myofilin (Mf) and downstream by CG3987 and CG3984. The tblastn search of D. melanogaster Glys-PC (query) against the D. simulans (GenBank Accession: GCA_000754195.3) Genome Assembly (database) placed the putative ortholog of Glys within scaffold CM002913 (CM002913.1) at locus LOC6728025 (XP_016034640.1)— with an E-value of 0.0 and a percent identity of 100.00%. Furthermore, the putative ortholog is flanked upstream by LOC6728023 (XP_016034621.1) and LOC6728024 (XP_044779336.1), which correspond to Gyc88E and Mf in D. melanogaster (E-value: 0.0 and 0.0; identity: 97.27% and 97.82%, respectively, as determined by blastp; Figure 1A, Altschul et al., 1990). The putative ortholog of Glys is flanked downstream by LOC6728026 (XP_002103378.1) and LOC6728027 (XP_016034642.1), which correspond to CG3987 and CG3984 in D. melanogaster (E-value: 0.0 and 6e-168; identity: 87.14% and 85.13%, respectively, as determined by blastp). The putative ortholog assignment for Glys in D. simulans is supported by the following evidence: The genes surrounding the Glys ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is completely conserved, supported by results generated from blastp, so we conclude that LOC6728025 is the correct ortholog of Glys in D. simulans (Figure 1A).
Protein Model
Glys in D. simulans has two unique protein-coding isoforms (Glys-PA and Glys-PC, identical to Glys-PB and Glys-PD; Figure 1B). mRNA isoforms Glys-RC, Glys-RB, and Glys-RD, which differ in their UTRs, contain four CDSs ,and isoform Glys-RA contains five CDSs. Relative to the ortholog in D. melanogaster, the RNA CDS number is conserved. The sequence of Glys-PC in D. simulans has 100.00% identity (E-value: 0.0) with the protein-coding isoform Glys-PC in D. melanogaster, as determined by blastp (Figure 1C). The dot plot of the ortholog with Glys-PA is exhibited in Figure 1D (E-value: 0.0; identity: 100.00%, as determined by blastp. Coordinates of this curated gene model (Glys-PA, Glys-PB, Glys-PC, Glys-PD) are stored by NCBI at GenBank/BankIt (accession BK064593, BK064594, BK064595, BK064596, respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).
","references":[{"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":null},{"reference":"Backlund AE, White J, Grillo L, Ianniello T, Swedrowski A, Yang M, Jemc J, Rele CP, 2024. Gene model for the ortholog of Glys in Drosophila busckii. microPublication Biology, submitted
","pubmedId":null,"doi":null},{"reference":"Bock IR, Wheeler MR. 1972. The Drosophila melanogaster species-group. The University of Texas Publication. 7213: 1-102. FBrf0024428.
","pubmedId":null,"doi":null},{"reference":"Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al., Celniker SE. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339): 473-9.
","pubmedId":"21179090","doi":null},{"reference":"Grewal SS. 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol 41(5): 1006-10.
","pubmedId":"18992839","doi":null},{"reference":"Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.
","pubmedId":"19694515","doi":null},{"reference":"Hu TT, Eisen MB, Thornton KR, Andolfatto P. 2013. A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 23(1): 89-98.
","pubmedId":"22936249","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":null},{"reference":"Koehler AC, Romo I, Le V, Youngblom JJ, Hark AT, Rele CP, Reed LK. 2024. Gene model for the ortholog of Glys in Drosophila yakuba. MicroPubl Biol 2024.
","pubmedId":null,"doi":"10.17912/micropub.biology.000983"},{"reference":"Lachaise D, Tsacas L. (1983). Breeding-sites of tropical African Drosophilids. Ashburner, Carson, Thompson, 1981-1986 3d: 221-332. FBrf0038884
","pubmedId":null,"doi":null},{"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":null},{"reference":"Lawson ME, Jones GM, Runion M, Sims D, Young A, Briggs O, et al., Reed LK. 2024. Gene model for the ortholog of ImpL2 in Drosophila simulans. MicroPubl Biol 2024.
","pubmedId":"39677518","doi":null},{"reference":"Lemeunier F, David J, Tsacas L, Ashburner M. 1986. The melanogaster species group. Ashburner, Carson, Thompson, 1981-1986 e: 147-256. FBrf0043749
","pubmedId":null,"doi":null},{"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":"Myers A, Hoffman A, Natysin M, Arsham AM, Stamm J, Thompson JS, Rele CP, Reed LK. 2024. Gene model for the ortholog Myc in Drosophila ananassae. MicroPubl Biol 2024.
","pubmedId":"39677519","doi":"10.17912/micropub.biology.000856"},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, et al., Kent WJ. 2021. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res 49(D1): D1046-D1057.
","pubmedId":"33221922","doi":null},{"reference":"Plyte SE, Hughes K, Nikolakaki E, Pulverer BJ, Woodgett JR. 1992. Glycogen synthase kinase-3: functions in oncogenesis and development. Biochim Biophys Acta 1114(2-3): 147-62.
","pubmedId":"1333807","doi":null},{"reference":"Powell JR. 1997. Progress and prospects in evolutionary biology: the Drosophila model. Oxford University Press, ISBN: 9780195076912
","pubmedId":null,"doi":null},{"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":null},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK. (2020). Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521
","pubmedId":null,"doi":"10.1101/2020.12.12.420521"},{"reference":"Roach PJ, Depaoli-Roach AA, Hurley TD, Tagliabracci VS. 2012. Glycogen and its metabolism: some new developments and old themes. Biochem J 441(3): 763-87.
","pubmedId":"22248338","doi":null},{"reference":"Sturtevant AH, 1919. A new species closely resembling Drosophila melanogaster. Psyche 26: 488-500. FBrf0000977
","pubmedId":null,"doi":null},{"reference":"Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.
","pubmedId":"16577879","doi":null},{"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":"Yamada T, Habara O, Yoshii Y, Matsushita R, Kubo H, Nojima Y, Nishimura T. 2019. The role of glycogen in development and adult fitness in Drosophila. Development 146(8).
","pubmedId":"30918052","doi":null}],"title":"Gene model for the ortholog of Glys in Drosophila simulans
","reviews":[],"curatorReviews":[{"curator":{"displayName":"Steven Marygold"},"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":"aerococcus","label":"Aerococcus","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":"dermacoccus nishinomiyaensis","label":"Dermacoccus nishinomiyaensis","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":"lactobacillus","label":"Lactobacillus","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":"ligilactobacillus","label":"Ligilactobacillus","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"ligilactobacillus salivarius","label":"Ligilactobacillus salivarius","imageSrc":"","imageAlt":"","mod":"","modLink":"","linkVariable":""},{"value":"limosilactobacillus","label":"Limosilactobacillus","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":"lontra longicaudis","label":"Lontra longicaudis","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":"stewartia floidana","label":"Stewartia floridana","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":"d5b60298-1938-4e21-a156-beecb1a49188","citedBy":[{"title":"Gene model for the ortholog of Glys in Drosophila ananassae","url":"https://doi.org/10.1101/2025.07.09.662856","datePublished":"July 2025","firstAuthor":"Gruys, ML"},{"title":"Gene model for the ortholog of Glyp in Drosophila pseudoobscura","url":"https://doi.org/10.1101/2025.07.18.665514","datePublished":"July 2025","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of Glyp in Drosophila ananassae","url":"https://doi.org/10.1101/2025.07.18.665411","datePublished":"July 2025","firstAuthor":"Bicanovsky, GN"},{"title":"Gene model for the ortholog of Pi3K21B in Drosophila eugracilis","url":"https://doi.org/10.1101/2025.07.21.665947","datePublished":"July 2025","firstAuthor":"Lieser, BC"},{"title":"Gene model for the ortholog of Ilp3 in Drosophila eugracilis","url":"https://doi.org/10.1101/2025.08.16.670678","datePublished":"August 2025","firstAuthor":"O’Brien, J"},{"title":"Gene model for the ortholog of gig in Drosophila mojavensis","url":"https://micropublication.org/journals/biology/micropub.biology.001027","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Gruys, ML"},{"title":"Gene model for the ortholog of Akt in Drosophila elegans","url":"https://doi.org/10.1101/2025.08.06.668967","datePublished":"August 2025","firstAuthor":"Dasgupta, J"},{"title":"Gene model for the ortholog of tgo in Drosophila miranda","url":"https://doi.org/10.1101/2025.08.04.668519","datePublished":"August 2025","firstAuthor":"Jones, GM"},{"title":"Gene model for the ortholog of tgo in Drosophila pseudoobscura","url":"https://doi.org/10.1101/2025.07.13.664599","datePublished":"July 2025","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of Ilp4 in Drosophila grimshawi","url":"https://doi.org/10.1101/2025.08.25.672213","datePublished":"August 2025","firstAuthor":"Cowan, R"},{"title":"Gene model for the ortholog of Pten in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.000901","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Jones, GM"},{"title":"Gene model for the ortholog of lin-28 in Drosophila mojavensis","url":"https://micropublication.org/journals/biology/micropub.biology.001096","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of Sdr in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001001","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Gruys, ML"},{"title":"Gene model for the ortholog of Mipp2 in Drosophila simulans","url":"https://micropublication.org/journals/biology/micropub.biology.000765","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Jones, GM"},{"title":"Gene model for the ortholog of dock in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001025","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of dock in Drosophila eugracilis","url":"https://micropublication.org/journals/biology/micropub.biology.001848","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Bicanovsky, GN"},{"title":"Gene model for the ortholog of S6k in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001030","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of Roc1a in Drosophila simulans","url":"https://micropublication.org/journals/biology/micropub.biology.001102","journal":"microPublication Biology","datePublished":"2025","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of gig in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001031","journal":"microPublication Biology","datePublished":"2026","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of Thor in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.000854","journal":"microPublication Biology","datePublished":"2026","firstAuthor":"Gruys, ML"},{"title":"Gene model for the ortholog of Ptp61F in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001002","journal":"microPublication Biology","datePublished":"2026","firstAuthor":"Backlund, AE"},{"title":"Gene Model for the ortholog of Ilp2 in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.000917","journal":"microPublication Biology","datePublished":"2026","firstAuthor":"Myers, AR"},{"title":"Gene model for the ortholog of Pi3K21B in Drosophila ananassae","url":"https://micropublication.org/journals/biology/micropub.biology.001009","journal":"microPublication Biology","datePublished":"2026","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of\n tgo\n in\n Drosophila persimilis","url":"https://doi.org/10.64898/2026.07.14.738511","datePublished":"July 2026","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of\n raptor\n in\n Drosophila eugracilis","url":"https://doi.org/10.64898/2026.07.10.737807","datePublished":"July 2026","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of\n raptor\n in\n Drosophila erecta","url":"https://doi.org/10.64898/2026.07.09.737526","datePublished":"July 2026","firstAuthor":"Backlund, AE"},{"title":"Gene model for the ortholog of\n raptor\n in\n Drosophila grimshawi","url":"https://doi.org/10.64898/2026.07.07.737051","datePublished":"July 2026","firstAuthor":"Lieser, BC"},{"title":"Gene model for the ortholog of\n tgo\n in\n Drosophila busckii","url":"https://doi.org/10.64898/2026.06.26.734908","datePublished":"July 2026","firstAuthor":"Perez, J"},{"title":"Gene model for the ortholog of\n Ilp4\n in\n Drosophila simulans","url":"https://doi.org/10.64898/2026.02.06.704405","datePublished":"February 2026","firstAuthor":"Laskowski, LF"},{"title":"Gene model for the ortholog of\n slmb\n in\n Drosophila pseudoobscura","url":"https://doi.org/10.64898/2026.01.07.698268","datePublished":"January 2026","firstAuthor":"Lawson, ME"},{"title":"Gene model for the ortholog of\n Ilp4\n in\n Drosophila eugracilis","url":"https://doi.org/10.1101/2025.09.05.674564","datePublished":"September 2025","firstAuthor":"Cowan, R"}],"parsedCsv":{"csvHeader":[],"csvData":[]}}}, "staticQueryHashes": ["2114697108"]}