{ "componentChunkName": "component---src-templates-article-page-js", "path": "/journals/biology/micropub-biology-000917", "result": {"data":{"article":{"manuscript":{"id":"216a260f-e1aa-4612-9841-43d603e8bcb6","submissionTypes":["new finding"],"citations":[],"doi":"10.17912/micropub.biology.000917","dbReferenceId":"","pmcId":"","pmId":"","proteopedia":"","reviewPanel":"","species":["drosophila"],"integrations":[],"corrections":null,"history":{"received":"2023-07-07T18:35:47.282Z","revisionReceived":"2026-08-20T19:31:44.071Z","accepted":"2026-08-27T06:18:48.130Z","published":"2026-08-29T02:43:23.609Z","indexed":"2026-09-12T02:43:23.609Z"},"versions":[{"id":"4683486d-a8ac-4400-a686-87972581ec2b","decision":"edit","abstract":"

Gene Model for the Ilp2 ortholog in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) assembly (GCA_000005115.1).

","acknowledgements":" We would like to thank Laura K. Reed and Wilson Leung, who created and maintain the GEP technological infrastructure.","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["University of Evansville, Evansville, IN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"js383@evansville.edu","firstName":"Joyce","lastName":"Stamm","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-8894-1897"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":true,"correspondingAuthor":true,"equalContribution":null,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.","image":{"url":"https://portal.micropublication.org/uploads/0965b6d69d896466cccf2f6f5954c0a5.png"},"imageCaption":"

(A) Synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as the Ilp2; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with exon depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; exon number is indicated along the top and right, and exons are also highlighted with alternating colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of exon two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"","methods":"

Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2020).

","reagents":"

","patternDescription":"\n

Introduction

\n

The insulin signaling pathway is a highly conserved pathway in animals and is central to nutrient uptake (Hietakangas and Cohen 2009; Grewal 2009). Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010; Laskowski et al., 2022). The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 (Drosophila 12 Genomes Consortium; GCA_000001215.4) in D. melanogaster from FB2022_03 (Larkin et al., 2021).

\n

D. ananassae 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 Doeschall (1858). D. ananassae is circumtropical (Markow and O’Grady 2006; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015; Lawson et al., 2023). The complete methods and dataset versions used to establish the gene model are described in Rele et al. (2020). The Genomics Education Partnership maintains a mirror of the UCSC Genome Browser (Kent WJ et al., 2002; Gonzalez et al., 2021), which is available at https://gander.wustl.edu.

\n

Synteny

\n

\tIlp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there’s a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster this is merely due to a short coding sequence.

\n

Protein Model

\n

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding exons. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding exons. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BKXXXXXX. These data are also available in Extended Data files below, which are archived in CaltechData.

\n

Special characteristics of the protein model

\n

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA’s overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol. 215: 403-10.","pubmedId":"2231712","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Bock, I.R., Wheeler, M.R. 1972. The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428.","pubmedId":"","doi":""},{"reference":"Brogiolo, W, Stocker, H, Ikeya, T, Rintelen, F, Fernandez, R, Hafen, E 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr. Biol. 11: 213-221.","pubmedId":"11250149","doi":"10.1016/s0960-9822(01)00068-9"},{"reference":"Doleschall, C.L. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie. 17: 73--128. FBrf0000091.","pubmedId":"","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 03-18.","pubmedId":"17994087","doi":"10.1038/nature06341"},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al, The FlyBase Consortium 2022. FlyBase: a guided tour of highlighted features. Genetics. 220: iyac035.","pubmedId":"335266522","doi":"10.1093/genetics/iyac035"},{"reference":"Grewal SS 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol. 41: 1006-10.","pubmedId":"18992839","doi":"10.1016/j.biocel.2008.10.010"},{"reference":"Grönke, Sebastian, Clarke, David-Francis, Broughton, Susan, Andrews, T Daniel, Partridge, Linda 2010. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet. 6: e1000857.","pubmedId":"20195512","doi":"10.1371/journal.pgen.1000857"},{"reference":"Hietakangas V, Cohen SM 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet. 2009;43: 389-410.","pubmedId":"19694515","doi":"10.1146/annurev-genet-102108-134815"},{"reference":"Ikeya, Tomoatsu, Galic, Milos, Belawat, Priyanka, Nairz, Knud, Hafen, Ernst 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine. Curr. Biol.. 12: 1293-1300.","pubmedId":"12176357","doi":"10.1016/s0960-9822(02)01043-6"},{"reference":"Kikkawa H 1938. Studies on the genetics and cytology of Drosophila ananassae. Genetica20. : 458–516.","pubmedId":"","doi":"https://doi.org/10.1007/BF01531779"},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J, FlyBase Consortium 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 49(D1): D899–D907.","pubmedId":"33219682","doi":"10.1093/nar/gkaa1026"},{"reference":"

Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP 2022. Drosophila simulans - Ilp2. MicroPubl. Biol. 2022

","pubmedId":"","doi":"10.17912/micropub.biology.000679"},{"reference":"

Lawson M.E., McAbee M., Lucas R.A., Tanner S., Wittke-Thompson J., Pelletier T.A., Ozsoy Z., Sterne-Marr R., Rele C.P. 2023. Drosophila ananassae – Ilp5. microPublication Biology. submitted.

","pubmedId":"","doi":""},{"reference":"

Markow, T.A., O’Grady, P. 2005. Drosophila: A guide to species identification and use. Academic Press 978-0-12-473052-6.

","pubmedId":"5073854","doi":"https://doi.org/10.1016/B978-012473052-6/50000-7"},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Kent WJ 2021. The UCSC Genome Browser database: 2021 update Nucleic Acids Res. Nucleic Acids Res. 49: D1046-D1057.","pubmedId":"33221922","doi":"10.1093/nar/gkaa1070"},{"reference":"Park, Sangbin, Alfa, Ronald W, Topper, Sydni M, Kim, Grace E S, Kockel, Lutz, Kim, Seung K 2014. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet. 10: e1004555.","pubmedId":"29187524","doi":"10.1371/journal.pgen.1004555"},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. Apr 1;30(7): 1003-5.","pubmedId":"24227676","doi":"10.1093/bioinformatics/btt637"},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol [version 1; peer review: 2 approved with reservations]. F1000Research. 11: 1579.","pubmedId":"","doi":"10.12688/f1000research.126839.1"},{"reference":"Ren, Suxia, Huang, Zengyi, Jiang, Yuqiang, Wang, Tao 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J. Cell Biol. : 517-526.","pubmedId":"29187524","doi":"10.1083/jcb.201706027"},{"reference":"Singh BN 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol. 48: 333-45.","pubmedId":"20726331","doi":""},{"reference":"Singh BN, Yadav JP 2015. Status of research on Drosophila ananassae at global level. J Genet. 94: 785-92.","pubmedId":"26690536","doi":"10.1007/s12041-015-0577-y"},{"reference":"Sturtevant AH 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A. 25: 137-41.","pubmedId":"16577879","doi":"10.1073/pnas.25.3.137"}],"title":"

Drosophila ananassae – Ilp2

","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"105b25d0-94d1-4115-969d-06f1e75a3a3b","decision":"revise","abstract":"

Gene Model for the Ilp2 ortholog in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) assembly (GCA_000005115.1).

","acknowledgements":" We would like to thank Laura K. Reed and Wilson Leung, who created and maintain the GEP technological infrastructure.","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["University of Evansville, Evansville, IN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"js383@evansville.edu","firstName":"Joyce","lastName":"Stamm","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-8894-1897"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":true,"correspondingAuthor":true,"equalContribution":null,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.","image":{"url":"https://portal.micropublication.org/uploads/0965b6d69d896466cccf2f6f5954c0a5.png"},"imageCaption":"

(A) Synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as the Ilp2; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with exon depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; exon number is indicated along the top and right, and exons are also highlighted with alternating colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of exon two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"","methods":"

Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2020).

","reagents":"

","patternDescription":"

Information to provide project, pathway, gene, and species context. This information may be repeated in multiple Drosophila ortholog gene model microPublications submitted by the Genome Education Partnership:

“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 lin-28 (lin-28) 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 insulin signaling pathway is a highly conserved pathway in animals and is central to nutrient uptake (Hietakangas and Cohen 2009; Grewal 2009).\"

\"Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010; Laskowski et al., 2022). \"

\"D. ananassae 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 Doeschall (1858). D. ananassae is circumtropical (Markow and O’Grady 2006; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015; Lawson et al., 2023).\"

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 (Drosophila 12 Genomes Consortium; GCA_000001215.4) in D. melanogaster from FB2022_03 (Larkin et al., 2021).

The complete methods and dataset versions used to establish the gene model are described in Rele et al. (2020). The Genomics Education Partnership maintains a mirror of the UCSC Genome Browser (Kent WJ et al., 2002; Gonzalez et al., 2021), which is available at https://gander.wustl.edu.

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there’s a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster this is merely due to a short coding sequence.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding exons. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding exons. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BKXXXXXX. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA’s overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol. 215: 403-10.","pubmedId":"2231712","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Bock, I.R., Wheeler, M.R. 1972. The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428.","pubmedId":"","doi":""},{"reference":"Brogiolo, W, Stocker, H, Ikeya, T, Rintelen, F, Fernandez, R, Hafen, E 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr. Biol. 11: 213-221.","pubmedId":"11250149","doi":"10.1016/s0960-9822(01)00068-9"},{"reference":"Doleschall, C.L. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie. 17: 73--128. FBrf0000091.","pubmedId":"","doi":""},{"reference":"Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 03-18.","pubmedId":"17994087","doi":"10.1038/nature06341"},{"reference":"Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, Dos Santos G, et al, The FlyBase Consortium 2022. FlyBase: a guided tour of highlighted features. Genetics. 220: iyac035.","pubmedId":"335266522","doi":"10.1093/genetics/iyac035"},{"reference":"Grewal SS 2009. Insulin/TOR signaling in growth and homeostasis: a view from the fly world. Int J Biochem Cell Biol. 41: 1006-10.","pubmedId":"18992839","doi":"10.1016/j.biocel.2008.10.010"},{"reference":"Grönke, Sebastian, Clarke, David-Francis, Broughton, Susan, Andrews, T Daniel, Partridge, Linda 2010. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet. 6: e1000857.","pubmedId":"20195512","doi":"10.1371/journal.pgen.1000857"},{"reference":"Hietakangas V, Cohen SM 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet. 2009;43: 389-410.","pubmedId":"19694515","doi":"10.1146/annurev-genet-102108-134815"},{"reference":"Ikeya, Tomoatsu, Galic, Milos, Belawat, Priyanka, Nairz, Knud, Hafen, Ernst 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine. Curr. Biol.. 12: 1293-1300.","pubmedId":"12176357","doi":"10.1016/s0960-9822(02)01043-6"},{"reference":"Kikkawa H 1938. Studies on the genetics and cytology of Drosophila ananassae. Genetica20. : 458–516.","pubmedId":"","doi":"https://doi.org/10.1007/BF01531779"},{"reference":"Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J, FlyBase Consortium 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 49(D1): D899–D907.","pubmedId":"33219682","doi":"10.1093/nar/gkaa1026"},{"reference":"

Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP 2022. Drosophila simulans - Ilp2. MicroPubl. Biol. 2022

","pubmedId":"","doi":"10.17912/micropub.biology.000679"},{"reference":"

Lawson M.E., McAbee M., Lucas R.A., Tanner S., Wittke-Thompson J., Pelletier T.A., Ozsoy Z., Sterne-Marr R., Rele C.P. 2023. Drosophila ananassae – Ilp5. microPublication Biology. submitted.

","pubmedId":"","doi":""},{"reference":"

Markow, T.A., O’Grady, P. 2005. Drosophila: A guide to species identification and use. Academic Press 978-0-12-473052-6.

","pubmedId":"5073854","doi":"https://doi.org/10.1016/B978-012473052-6/50000-7"},{"reference":"Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Kent WJ 2021. The UCSC Genome Browser database: 2021 update Nucleic Acids Res. Nucleic Acids Res. 49: D1046-D1057.","pubmedId":"33221922","doi":"10.1093/nar/gkaa1070"},{"reference":"Park, Sangbin, Alfa, Ronald W, Topper, Sydni M, Kim, Grace E S, Kockel, Lutz, Kim, Seung K 2014. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet. 10: e1004555.","pubmedId":"29187524","doi":"10.1371/journal.pgen.1004555"},{"reference":"Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. Apr 1;30(7): 1003-5.","pubmedId":"24227676","doi":"10.1093/bioinformatics/btt637"},{"reference":"Rele CP, Sandlin KM, Leung W, Reed LK 2022. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol [version 1; peer review: 2 approved with reservations]. F1000Research. 11: 1579.","pubmedId":"","doi":"10.12688/f1000research.126839.1"},{"reference":"Ren, Suxia, Huang, Zengyi, Jiang, Yuqiang, Wang, Tao 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J. Cell Biol. : 517-526.","pubmedId":"29187524","doi":"10.1083/jcb.201706027"},{"reference":"Singh BN 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol. 48: 333-45.","pubmedId":"20726331","doi":""},{"reference":"Singh BN, Yadav JP 2015. Status of research on Drosophila ananassae at global level. J Genet. 94: 785-92.","pubmedId":"26690536","doi":"10.1007/s12041-015-0577-y"},{"reference":"Sturtevant AH 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A. 25: 137-41.","pubmedId":"16577879","doi":"10.1073/pnas.25.3.137"}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[{"reviewer":{"displayName":"David Molik"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"02c6c1ec-765b-4900-84c7-2637f5bc11df","decision":"edit","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the 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. This article was prepared while Joyce Stamm was employed at the University of Evansville. The opinions expressed in this article are the author's own and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["University of Evansville, Evansville, IN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"joyce.stamm@nih.gov","firstName":"Joyce","lastName":"Stamm","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-8894-1897"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":true,"correspondingAuthor":true,"equalContribution":null,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/0965b6d69d896466cccf2f6f5954c0a5.png"},"imageCaption":"

(A) Synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as the Ilp2; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (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. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae.

","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 target gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly (D. ananassae (GCA_000005115.1 - Drosophila 12 Genomes Consortium) 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 reference gene 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 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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O’Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., in press).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 (Drosophila 12 Genomes Consortium; GCA_000001215.4) in D. melanogaster from FB2022_03 (Larkin et al., 2021).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there’s a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster this is merely due to a short coding sequence.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA’s overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","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":""},{"reference":"

Bock IR, Wheeler MR. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1--102. FBrf0024428

","pubmedId":"","doi":""},{"reference":"

Brogiolo W, Stocker H, Ikeya T, Rintelen F, Fernandez R, Hafen E. 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 11(4): 213-21.

","pubmedId":"11250149","doi":""},{"reference":"

Doleschall CL. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie 17: 73--128. FBrf0000091

","pubmedId":"","doi":""},{"reference":"

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.

","pubmedId":"17994087","doi":""},{"reference":"

Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G Goodman JL, Goutte-Gattat D, Jenkins V, Kaufman T, Larkin A, Matthews B, Millburn G, Strelets VB, and the FlyBase Consortium (2022) FlyBase: a guided tour of highlighted features. Genetics, Volume 220, Issue 4, April 2022.

","pubmedId":"","doi":"https://doi.org/10.1093/genetics/iyac035"},{"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":""},{"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":""},{"reference":"

Grönke S, Clarke DF, Broughton S, Andrews TD, Partridge L. 2010. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet 6(2): e1000857.

","pubmedId":"20195512","doi":""},{"reference":"

Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

","pubmedId":"19694515","doi":""},{"reference":"

Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

","pubmedId":"19694515","doi":""},{"reference":"

Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol 12(15): 1293-300.

","pubmedId":"12176357","doi":""},{"reference":"

Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.

","pubmedId":"35980571","doi":""},{"reference":"

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res 12(6): 996-1006.

","pubmedId":"12045153","doi":""},{"reference":"

Kikkawa H. 1938 Studies on the genetics and cytology of Drosophila ananassae. Genetica20, 458–516.

","pubmedId":"","doi":"https://doi.org/10.1007/BF01531779"},{"reference":"

Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.

","pubmedId":"33219682","doi":""},{"reference":"

Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP (2022). Drosophila simulans - Ilp2. microPublication Biology.

","pubmedId":"","doi":"https://doi.org/10.17912/micropub.biology.000679"},{"reference":"

Lawson ME, McAbee M, Lucas RA, Tanner S, Wittke-Thompson J, Pelletier TA, Ozsoy Z, Sterne-Marr R, Rele CP. 2024. Gene model for the ortholog of Ilp5 in Drosophila ananassae, microPublication Biology, submitted

","pubmedId":"","doi":""},{"reference":"

Markow TA and O’Grady P. (2005) Drosophila: A guide to species identification and use. 978-0-12-473052-6

","pubmedId":"","doi":""},{"reference":"

Myers A., Hoffmann A., Natysin M., Arsham A.M, Stamm J., Thompson J.S., Rele C.P. 2024. Gene model for the ortholog of Myc in Drosophila ananassae, microPublication Biology (in press)


","pubmedId":"","doi":""},{"reference":"

Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.

","pubmedId":"27773922","doi":""},{"reference":"

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":""},{"reference":"

Park S, Alfa RW, Topper SM, Kim GE, Kockel L, Kim SK. 2014. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet 10(8): e1004555.

","pubmedId":"25101872","doi":""},{"reference":"

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.

","pubmedId":"24227676","doi":""},{"reference":"

Rele CP, Sandlin KM, Leung W, Reed LK. 2023. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Research 11: 1579.

","pubmedId":"","doi":"https://doi.org/10.12688/f1000research.126839.2"},{"reference":"

Ren S, Huang Z, Jiang Y, Wang T. 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol 217(2): 517-526.

","pubmedId":"29187524","doi":""},{"reference":"

Singh BN, Yadav JP. 2015. Status of research on Drosophila ananassae at global level. J Genet 94(4): 785-92.

","pubmedId":"26690536","doi":""},{"reference":"

Singh BN. 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol 48(4): 333-45.

","pubmedId":"20726331","doi":""},{"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":""},{"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":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"7339cf23-c453-478c-8cc0-0cd9e42b8aca","decision":"revise","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the 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. This article was prepared while Joyce Stamm was employed at the University of Evansville. The opinions expressed in this article are the author's own and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["University of Evansville, Evansville, IN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"joyce.stamm@nih.gov","firstName":"Joyce","lastName":"Stamm","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-8894-1897"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":true,"correspondingAuthor":true,"equalContribution":null,"WBId":null,"orcid":"0000-0002-3473-9319"}],"awards":[],"conflictsOfInterest":null,"dataTable":null,"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/0965b6d69d896466cccf2f6f5954c0a5.png"},"imageCaption":"

(A) Synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as the Ilp2; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (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. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae

","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 target gene for a given isoform and run it using tblastn against their target Drosophila species genome assembly (D. ananassae (GCA_000005115.1 - Drosophila 12 Genomes Consortium) 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 reference gene model. At least two independent models for this gene were generated by students under the 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 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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O’Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., in press).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 (Drosophila 12 Genomes Consortium; GCA_000001215.4) in D. melanogaster from FB2022_03 (Larkin et al., 2021).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there’s a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster this is merely due to a short coding sequence.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA’s overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","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.

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Brogiolo W, Stocker H, Ikeya T, Rintelen F, Fernandez R, Hafen E. 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 11(4): 213-21.

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Doleschall CL. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie 17: 73-128. FBrf0000091

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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.

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Grönke S, Clarke DF, Broughton S, Andrews TD, Partridge L. 2010. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet 6(2): e1000857.

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Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

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Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol 12(15): 1293-300.

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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.

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Kikkawa H. 1938 Studies on the genetics and cytology of Drosophila ananassae. Genetica20, 458–516.

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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.

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Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP (2022). Drosophila simulans - Ilp2. microPublication Biology.

","pubmedId":"","doi":"10.17912/micropub.biology.000679"},{"reference":"

Lawson ME, McAbee M, Lucas RA, Tanner S, Wittke-Thompson J, Pelletier TA, et al., Reed LK. 2024. Gene model for the ortholog of Ilp5 in Drosophila ananassae. MicroPubl Biol 2024.

","pubmedId":"39717145","doi":""},{"reference":"

Markow TA and O’Grady P. (2005) Drosophila: A guide to species identification and use. 978-0-12-473052-6

","pubmedId":"","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":""},{"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":"

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":""},{"reference":"

Park S, Alfa RW, Topper SM, Kim GE, Kockel L, Kim SK. 2014. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet 10(8): e1004555.

","pubmedId":"25101872","doi":""},{"reference":"

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al., Kent WJ. 2014. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30(7): 1003-5.

","pubmedId":"24227676","doi":""},{"reference":"

Rele CP, Sandlin KM, Leung W, Reed LK. 2023. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Research 11: 1579.

","pubmedId":"","doi":"10.12688/f1000research.126839.2"},{"reference":"

Ren S, Huang Z, Jiang Y, Wang T. 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol 217(2): 517-526.

","pubmedId":"29187524","doi":""},{"reference":"

Singh BN, Yadav JP. 2015. Status of research on Drosophila ananassae at global level. J Genet 94(4): 785-92.

","pubmedId":"26690536","doi":""},{"reference":"

Singh BN. 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol 48(4): 333-45.

","pubmedId":"20726331","doi":""},{"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":""},{"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":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[{"reviewer":{"displayName":"Rebecca Spokony"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"6bde01a2-01da-458f-ae3a-8ecb2be7c5f4","decision":"edit","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. Also, thank you to Madeline Gruys and Logan Cohen for assistance in updating the manuscript to the current template.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":null,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["conceptualization","fundingAcquisition","methodology","project","supervision","validation","visualization"],"email":"lreed1@ua.edu","firstName":"Laura","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"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":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/98616cdbb44796cfcd77731e07e08e06.png"},"imageCaption":"

(A) A diagram of synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as Ilp2; while gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). Note that the RNAseq for embryos show now alignment of expression data at this locus, suggesting that this gene may not expressed in embryos in this species; which neither supports or refutes the proposed model. Further note that the lack of an aligned Spaln D. melanogaster protein at this position indicates that the degree of sequence divergence between the reference gene and the target gene is greater that then minimum similarity needed to see an alignment for this algorithm. By default, Spaln is less sensitive and more specific than BLAST for assigning alignments. (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; while CDS number is indicated along the top and right, and CDSs are also highlighted with alternating background colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae

","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/genechecker/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 (Gruys et al., 2025).

","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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O'Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., 2024).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 in D. melanogaster from FB2022_03 (Larkin et al., 2021; Gramates et al., 2022; Jenkins et al., 2022).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there's a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA's overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","references":[{"reference":"

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Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol 12(15): 1293-300.

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Kikkawa H. 1938 Studies on the genetics and cytology of Drosophila ananassae. Genetica20, 458–516.

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Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP (2022). Drosophila simulans - Ilp2. microPublication Biology.

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Lawson ME, McAbee M, Lucas RA, Tanner S, Wittke-Thompson J, Pelletier TA, et al., Reed LK. 2024. Gene model for the ortholog of Ilp5 in Drosophila ananassae. MicroPubl Biol 2024.

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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.

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Singh BN. 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol 48(4): 333-45.

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Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.

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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":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"e9294929-c780-4343-843f-4170bf7cf0c2","decision":"revise","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. Also, thank you to Madeline Gruys and Logan Cohen for assistance in updating the manuscript to the current template.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":null,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["conceptualization","fundingAcquisition","methodology","project","supervision","validation","visualization"],"email":"lreed1@ua.edu","firstName":"Laura","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"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":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/98616cdbb44796cfcd77731e07e08e06.png"},"imageCaption":"

(A) A diagram of synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as Ilp2; while gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). Note that the RNAseq for embryos show now alignment of expression data at this locus, suggesting that this gene may not expressed in embryos in this species; which neither supports or refutes the proposed model. Further note that the lack of an aligned Spaln D. melanogaster protein at this position indicates that the degree of sequence divergence between the reference gene and the target gene is greater that then minimum similarity needed to see an alignment for this algorithm. By default, Spaln is less sensitive and more specific than BLAST for assigning alignments. (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; while CDS number is indicated along the top and right, and CDSs are also highlighted with alternating background colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae

","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/genechecker/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 (Gruys et al., 2025).

","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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O'Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., 2024).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 in D. melanogaster from FB2022_03 (Larkin et al., 2021; Gramates et al., 2022; Jenkins et al., 2022).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there's a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA's overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","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.

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Doleschall CL. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie 17: 73-128. FBrf0000091

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","pubmedId":"","doi":"10.1093/genetics/iyac035"},{"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.

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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.

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Gruys ML, Sharp MA, Lill Z, Xiong C, Hark AT, Youngblom JJ, Rele CP, Reed LK. 2025. Gene model for the ortholog of Glys in Drosophila simulans. MicroPubl Biol 2025: 10.17912/micropub.biology.001168.

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Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

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Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

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Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol 12(15): 1293-300.

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Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.

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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.

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Kikkawa H. 1938 Studies on the genetics and cytology of Drosophila ananassae. Genetica20, 458–516.

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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.

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Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP (2022). Drosophila simulans - Ilp2. microPublication Biology.

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Lawson ME, McAbee M, Lucas RA, Tanner S, Wittke-Thompson J, Pelletier TA, et al., Reed LK. 2024. Gene model for the ortholog of Ilp5 in Drosophila ananassae. MicroPubl Biol 2024.

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Markow TA and O’Grady P. (2005) Drosophila: A guide to species identification and use. 978-0-12-473052-6

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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.

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Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.

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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.

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Rele CP, Sandlin KM, Leung W, Reed LK. 2023. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Research 11: 1579.

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Ren S, Huang Z, Jiang Y, Wang T. 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol 217(2): 517-526.

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Singh BN, Yadav JP. 2015. Status of research on Drosophila ananassae at global level. J Genet 94(4): 785-92.

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Singh BN. 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol 48(4): 333-45.

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Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.

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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":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[{"reviewer":{"displayName":"Rebecca Spokony"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":null}]},{"id":"d381eda6-db6b-495b-8037-c8ab300b0c5b","decision":"accept","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. Also, thank you to Madeline Gruys and Logan Cohen for assistance in updating the manuscript to the current template.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":null,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["conceptualization","fundingAcquisition","methodology","project","supervision","validation","visualization"],"email":"lreed1@ua.edu","firstName":"Laura","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"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":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/98616cdbb44796cfcd77731e07e08e06.png"},"imageCaption":"

(A) A diagram of synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as Ilp2; while gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). Note that the RNAseq for embryos shows no alignment of expression data at this locus, suggesting that this gene may not be expressed in embryos in this species, which neither supports or refutes the proposed model. Further note that the lack of an aligned Spaln D. melanogaster protein at this position indicates that the degree of sequence divergence between the reference gene and the target gene is greater than the minimum similarity needed to see an alignment for this algorithm. By default, Spaln is less sensitive and more specific than BLAST for assigning alignments. (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; while CDS number is indicated along the top and right, and CDSs are also highlighted with alternating background colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae

","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/genechecker/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 (Gruys et al., 2025).

","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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O'Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., 2024).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 in D. melanogaster from FB2022_03 (Larkin et al., 2021; Gramates et al., 2022; Jenkins et al., 2022).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there's a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA's overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","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":""},{"reference":"

Bock IR, Wheeler MR. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1-102. FBrf0024428

","pubmedId":"","doi":""},{"reference":"

Brogiolo W, Stocker H, Ikeya T, Rintelen F, Fernandez R, Hafen E. 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 11(4): 213-21.

","pubmedId":"11250149","doi":""},{"reference":"

Doleschall CL. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie 17: 73-128. FBrf0000091

","pubmedId":"","doi":""},{"reference":"

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.

","pubmedId":"17994087","doi":""},{"reference":"

Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, et al., Lovato. 2022. FlyBase: a guided tour of highlighted features. Genetics 220: 10.1093/genetics/iyac035.

","pubmedId":"","doi":"10.1093/genetics/iyac035"},{"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":""},{"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":""},{"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":""},{"reference":"

Grönke S, Clarke DF, Broughton S, Andrews TD, Partridge L. 2010. Molecular evolution and functional characterization of Drosophila insulin-like peptides. PLoS Genet 6(2): e1000857.

","pubmedId":"20195512","doi":""},{"reference":"

Gruys ML, Sharp MA, Lill Z, Xiong C, Hark AT, Youngblom JJ, Rele CP, Reed LK. 2025. Gene model for the ortholog of Glys in Drosophila simulans. MicroPubl Biol 2025: 10.17912/micropub.biology.001168.

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Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

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Hietakangas V, Cohen SM. 2009. Regulation of tissue growth through nutrient sensing. Annu Rev Genet 43: 389-410.

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Ikeya T, Galic M, Belawat P, Nairz K, Hafen E. 2002. Nutrient-dependent expression of insulin-like peptides from neuroendocrine cells in the CNS contributes to growth regulation in Drosophila. Curr Biol 12(15): 1293-300.

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Jenkins VK, Larkin A, Thurmond J, FlyBase Consortium. 2022. Using FlyBase: A Database of Drosophila Genes and Genetics. Methods Mol Biol 2540: 1-34.

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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.

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Kikkawa H. 1938 Studies on the genetics and cytology of Drosophila ananassae. Genetica20, 458–516.

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Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, et al., FlyBase Consortium. 2021. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 49(D1): D899-D907.

","pubmedId":"33219682","doi":""},{"reference":"

Laskowski, LF; Kiser, CA; Huber, R; Kusche, S; Arsham, AM; Giarla, TC; Rele, CP (2022). Drosophila simulans - Ilp2. microPublication Biology.

","pubmedId":"","doi":"10.17912/micropub.biology.000679"},{"reference":"

Lawson ME, McAbee M, Lucas RA, Tanner S, Wittke-Thompson J, Pelletier TA, et al., Reed LK. 2024. Gene model for the ortholog of Ilp5 in Drosophila ananassae. MicroPubl Biol 2024.

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Markow TA and O’Grady P. (2005) Drosophila: A guide to species identification and use. 978-0-12-473052-6

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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":""},{"reference":"

Mudge JM, Harrow J. 2016. The state of play in higher eukaryote gene annotation. Nat Rev Genet 17(12): 758-772.

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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.

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Park S, Alfa RW, Topper SM, Kim GE, Kockel L, Kim SK. 2014. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion. PLoS Genet 10(8): e1004555.

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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.

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Rele CP, Sandlin KM, Leung W, Reed LK. 2023. Manual annotation of Drosophila genes: a Genomics Education Partnership protocol. F1000Research 11: 1579.

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Ren S, Huang Z, Jiang Y, Wang T. 2018. dTBC1D7 regulates systemic growth independently of TSC through insulin signaling. J Cell Biol 217(2): 517-526.

","pubmedId":"29187524","doi":""},{"reference":"

Singh BN, Yadav JP. 2015. Status of research on Drosophila ananassae at global level. J Genet 94(4): 785-92.

","pubmedId":"26690536","doi":""},{"reference":"

Singh BN. 2010. Drosophila ananassae: a good model species for genetical, behavioural and evolutionary studies. Indian J Exp Biol 48(4): 333-45.

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Sturtevant AH. 1939. On the Subdivision of the Genus Drosophila. Proc Natl Acad Sci U S A 25(3): 137-41.

","pubmedId":"16577879","doi":""},{"reference":"

Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, et al., Micklos DA. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One 14(10): e0224086.

","pubmedId":"31658277","doi":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

","reviews":[],"curatorReviews":[{"curator":{"displayName":"FlyBase Curators"},"openAcknowledgement":false,"submitted":"1787729582309"}]},{"id":"ea8efd15-b38c-4307-9fe6-38e6db31fce8","decision":"publish","abstract":"

Gene model for the ortholog of Insulin-like peptide 2 (Ilp2) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae. 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":"

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models. Also, thank you to Madeline Gruys and Logan Cohen for assistance in updating the manuscript to the current template.

","authors":[{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["formalAnalysis","validation","writing_originalDraft","writing_reviewEditing"],"email":"amyers24@crimson.ua.edu","firstName":"Abigail R. ","lastName":"Myers","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-4329-0277"},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["formalAnalysis","writing_reviewEditing"],"email":"robyn.huber119@gmail.com","firstName":"Robyn","lastName":"Huber","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":""},{"affiliations":["Bemidji State University, Bemidji, MN USA"],"departments":[""],"credit":["supervision","writing_reviewEditing"],"email":"aarsham@bemidjistate.edu","firstName":"Andrew M","lastName":"Arsham","submittingAuthor":null,"correspondingAuthor":null,"equalContribution":null,"WBId":null,"orcid":"0000-0002-5274-8710"},{"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":null,"WBId":null,"orcid":"0000-0002-3473-9319"},{"affiliations":["The University of Alabama, Tuscaloosa, AL USA"],"departments":[""],"credit":["conceptualization","fundingAcquisition","methodology","project","supervision","validation","visualization"],"email":"lreed1@ua.edu","firstName":"Laura","lastName":"Reed","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":false,"WBId":null,"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":"

The authors declare that there are no conflicts of interest present.

","dataTable":{"url":null},"extendedData":[{"description":"GFF, FASTA, and PEP of the model","doi":null,"resourceType":"Model","name":"DanaCAF1_Ilp2.zip","url":"https://portal.micropublication.org/uploads/d250dd7c56bc5d0aa27e4b0bf2090199.zip"}],"funding":"

This material is based upon work supported by the National Science Foundation under Grant No. IUSE-1915544 to LKR and the National Institute of General Medical Sciences of the National Institutes of Health Award R25GM130517 to LKR. The Genomics Education Partnership is fully financed by Federal moneys. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

","image":{"url":"https://portal.micropublication.org/uploads/98616cdbb44796cfcd77731e07e08e06.png"},"imageCaption":"

(A) A diagram of synteny of genomic neighborhood of Ilp2 in D. melanogaster and D. ananassae. Gene arrows pointing in the same direction as Ilp2 in both D. ananassae and D. melanogaster are on the same strand as Ilp2; while gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp2 is on the + strand in D. melanogaster; arrows pointing to the left indicate that Ilp2 is on the – strand in D. ananassae. White arrows in D. ananassae indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. The gene names given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. ananassae. (B) Gene Model in UCSC Track Hub (Raney et al. 2014): the gene model in D. ananassae (black), Spaln of D. melanogaster Proteins (purple, alignment of refseq proteins from D. melanogaster), BLAT alignments of NCBI RefSeq Genes (blue, alignment of refseq genes for D. ananassae), RNA-Seq from Adult Females (red), Adult Males (blue), RNA-Seq for Wolbachia-cured Embryo (pink), alignment of Illumina RNAseq reads from D. ananassae), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952). The splice junction shown has a read-depth of 1777 with red supporting splice junctions having a range of >1000. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). Note that the RNAseq for embryos shows no alignment of expression data at this locus, suggesting that this gene may not be expressed in embryos in this species, which neither supports or refutes the proposed model. Further note that the lack of an aligned Spaln D. melanogaster protein at this position indicates that the degree of sequence divergence between the reference gene and the target gene is greater than the minimum similarity needed to see an alignment for this algorithm. By default, Spaln is less sensitive and more specific than BLAST for assigning alignments. (C) Dot Plot of Ilp2-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. ananassae (y-axis). Amino acid number is indicated along the left and bottom; while CDS number is indicated along the top and right, and CDSs are also highlighted with alternating background colors. There are two large regions of sequence dissimilarity as displayed by the red (1) and blue (2) boxes. There is also one indel in the middle of CDS two represented by parallel lines. (D) The protein alignment of Ilp2-PA in D. ananassae against Ilp2-PA in D. melanogaster is shown. Boxes 1 and 2 correspond to the similarly labeled boxes in the Dot Plot highlighting regions of sequence dissimilarity.

","imageTitle":"

Genomic neighborhood and gene model for Ilp2 in D. ananassae

","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/genechecker/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 (Gruys et al., 2025).

","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).

“Insulin-like peptide 2 (Ilp2), a core component of the insulin signaling pathway, mediates growth by acting as a ligand for the Insulin Receptor (InR) and transducing a signal via the Chico/PI3K/Akt(PKB) pathway (Brogiolo et al., 2001; Park et al., 2014). Ilp2 plays a role in regulating body size by increasing the size and number of cells in individual organs (Ren et al., 2017). Evolutionary studies have shown that loss of Ilp2 increases lifespan and changes in expression may have contributed to the evolution of body size in the Hawaiian Drosophila species (Grönke et al., 2010). In the absence of Ilp2, over-expression of Ilp1 and Ilp3-7 is enough to promote growth in Drosophila (Ikeya et al., 2002). Ilp2 mutants also seem to have severe developmental delay (Grönke et al., 2010).” (Laskowski et al., 2022).

“D. ananassae (NCBI:txid7217) 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 Doleschall (1858). D. ananassae is circumtropical (Markow and O'Grady 2005; https://www.taxodros.uzh.ch, accessed 1 Feb 2023), and often associated with human settlement (Singh 2010). It has been extensively studied as a model for its cytogenetic and genetic characteristics, and in experimental evolution (Kikkawa 1938; Singh and Yadav 2015).” (Lawson et al., 2024).

The model presented here is the ortholog of Ilp2 in the May 2011 (Agencourt dana_caf1/DanaCAF1) assembly of D. ananassae (Drosophila 12 Genomes Consortium 2007; GCA_000005115.1) and corresponds to the Gnomon Peptide ID (XP_001956274.1) predicted model in D. ananassae (LOC6507309). This gene model is based on RNA-Seq data from D. ananassae (Graveley et al, 2011; SRP006203, SRP007906, PRJNA257286, PRJNA388952) and the Ilp2 in D. melanogaster from FB2022_03 (Larkin et al., 2021; Gramates et al., 2022; Jenkins et al., 2022).

Synteny

Ilp2 occurs on Chromosome 3L in D. melanogaster and is flanked by Zasp67 and Ilp1 upstream. Ilp2 is nested in CG32052 along with Ilp3 and Ilp4 to the right. Downstream, Ilp2 is flanked by CG43897 (which nests Ilp5) and I-2. We determined that the putative ortholog of Ilp2 is found on scaffold_13337 (CH902618.1) in D. ananassae with LOC6507309 (via tblastn search with an e-value of 3e-18 and percent identity of 42.70%), where it is flanked by LOC6507753 (XP_014765450.1) and LOC6507308 (XP_001956275.2) which correspond to Zasp67 and Ilp1 in D. melanogaster with e-values 0.0 and 4e-24 and percent identities 67.67% and 52.46% respectively as determined by blastp (Figure 1A, Altschul et al., 1990). Ilp2 is nested in LOC6507310 (XP_001956271.2) which corresponds to CG32052 in D. melanogaster with an e-value of 0.0 and a percent identity of 86.67% as determined by blastp. Nested in CG32052 downstream of Ilp2 are genes LOC6507752 (XP_001956273.1) and LOC6507751 (XP_032309882.1) which correspond to Ilp3 and Ilp4 in D. melanogaster with e-values of 1e-21 and 7e-28 and percent identities 46.32% and 48.91% respectively, as determined by blastp. Downstream of Ilp2 is LOC6507311 (XP_044570593.1) (which nests LOC6502822 (XP_001956270.1) and LOC6507750 (XP_001956268.3) which correspond to CG43897, Ilp5, and I-2 in D. melanogaster with e-values 0.0, 8e-09, and 1e-84 and percent identities 68.85%, 39.51%, and 72.50% respectively, as determined by blastp. We suggest this is the correct ortholog assignment for Ilp2 in D. ananassae because local synteny is conserved and although there's a low percent similarity (46.79%) between Ilp2-PA in D. ananassae and Ilp2-PA in D. melanogaster.

Protein Model

Ilp2 in D. ananassae has one protein coding isoform (Ilp2-PA) (Figure 1B). Isoform (Ilp2-PA) contains two protein coding CDSs. Similarly, Ilp2 in D. melanogaster has one protein coding isoform (Ilp2-PA) with two coding CDSs. The sequence of Ilp2-PA in D. ananassae has 46.79% identity with Ilp2-PA in D. melanogaster as determined by blastp (Figure 1C). There are large portions of sequence dissimilarity throughout the gene model as indicated by the red and blue boxes in the Dot Plot (Figure 1C). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accession BK064414. These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Sequence dissimilarity in gene model: The regions of sequence dissimilarity are highlighted with boxes in the Dot Plot (Figure 1C) and protein alignment (Figure 1D). Although these regions appear to be large, Ilp2-PA's overall short coding sequence amplifies the length of the gaps in the Dot Plot.

","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":""},{"reference":"

Bock IR, Wheeler MR. (1972). The Drosophila melanogaster species group. Univ. Texas Publs Stud. Genet. 7(7213): 1-102. FBrf0024428

","pubmedId":"","doi":""},{"reference":"

Brogiolo W, Stocker H, Ikeya T, Rintelen F, Fernandez R, Hafen E. 2001. An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 11(4): 213-21.

","pubmedId":"11250149","doi":""},{"reference":"

Doleschall CL. 1858. Derde bijdrage tot de kennis der Dipteren fauna van nederlandsch indie. Natuurk. Tijd. Ned.-Indie 17: 73-128. FBrf0000091

","pubmedId":"","doi":""},{"reference":"

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al., MacCallum I. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450(7167): 203-18.

","pubmedId":"17994087","doi":""},{"reference":"

Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, et al., Lovato. 2022. FlyBase: a guided tour of highlighted features. Genetics 220: 10.1093/genetics/iyac035.

","pubmedId":"","doi":"10.1093/genetics/iyac035"},{"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":""},{"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":""},{"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.

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","pubmedId":"31658277","doi":""}],"title":"

Gene Model for the ortholog of Ilp2 in Drosophila ananassae

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