Gene model for the ortholog of Ilp4 in Drosophila eugracilis

Gene model for the ortholog of Ilp4 in Drosophila eugracilis | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Gene model for the ortholog of Ilp4 in Drosophila eugracilis View ORCID Profile Rachael Cowan , Amun Uppal , Clairine I. S. Larsen , View ORCID Profile Christopher E. Ellison , View ORCID Profile Nicole S. Torosin , View ORCID Profile Jeffrey S. Thompson , View ORCID Profile Chinmay P. Rele , View ORCID Profile Lori Boies doi: https://doi.org/10.1101/2025.09.05.674564 Rachael Cowan 1 The University of Alabama , Tuscaloosa, AL, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Rachael Cowan Amun Uppal 2 Rutgers University , New Brunswick, NJ USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site Clairine I. S. Larsen 3 Denison University , Granville, OH, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site Christopher E. Ellison 2 Rutgers University , New Brunswick, NJ USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Christopher E. Ellison Nicole S. Torosin 2 Rutgers University , New Brunswick, NJ USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Nicole S. Torosin Jeffrey S. Thompson 3 Denison University , Granville, OH, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jeffrey S. Thompson Chinmay P. Rele 1 The University of Alabama , Tuscaloosa, AL, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Chinmay P. Rele Lori Boies 4 St. Mary’s University , San Antonio, TX, USA Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Lori Boies For correspondence: lboies{at}stmarytx.edu Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract Gene Model for Insulin-like peptide 4 ( Ilp4) in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2). The characterization of this ortholog was carried out as part of a larger, ongoing dataset designed to explore the evolution of the insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila , utilizing the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences. Introduction This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org ) for Course-based Undergraduate Research Experience (CURE). The following information in quotes may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster genes in the insulin signaling pathway. There are eight insulin-like peptides in Drosophila which act on the insulin receptor to trigger the Insulin-like Receptor (IR) signaling pathway (Guirao-Rico et al ., 2010; Brogiolo et al ., 2001 ). This family of peptides affects growth and metabolism in Drosophila and has been found to impact female sleep and mating behavior ( Wu and Brown, 2005 ; Wigby et al ., 2011 ; Newell et al ., 2020 ). Ilp4 is highly expressed in embryonic mesoderm and midgut and larval midgut ( Brogiolo et al ., 2001 ). Grönke et al . found that out of the insulin-like peptides 1-7, Ilp4 is the most conserved between Drosophila species after Ilp7 (2010). Despite this conservation, little is known about the specific function of Ilp4. We propose a gene model for the D. eugracilis ortholog of the D. melanogaster Insulin-like peptide 4 (Ilp4) gene. The genomic region of the ortholog corresponds to the uncharacterized protein LOC108114483 (RefSeq accession XP_017080990.1) in the Deug_2.0 Genome Assembly of D. eugracilis (GenBank Accession: GCA_000236325.2 - Chen et al., 2014 ). This model is based on RNA-Seq data from D. eugracilis (PRJNA63469) and Ilp4 in D. melanogaster using FlyBase release FB2022_04 (GCA_000001215.4; Larkin et al., 2021). D. eugracilis is part of the melanogaster species group within the subgenus Sophophora of the genus Drosophila ( Pélandakis et al., 1993 ). It was first described as Tanygastrella gracilis by Duda (1924) and revised to Drosophila eugracilis by Bock and Wheeler (1972) . D. eugracilis is found in humid tropical and subtropical forests across southeast Asia ( Morgan et al., 2022 ). “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, the fruit fly Drosophila melanogaster. This allows 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 ). Results Synteny The target gene, Ilp4 , occurs on chromosome 3L in D. melanogaster is nested within CG32052 alongside Insulin-like peptide 3 ( Ilp3 ) and Insulin-like peptide 2 ( Ilp2 ). Ilp4 is flanked upstream by Cyclin-dependent kinase 8 ( Cdk8 ), Inhibitor-2 ( I-2 ), and Insulin-like peptide 5 (Ilp5) which is nested by CG43897. Ilp4 is flanked downstream by Insulin-like peptide 1 ( Ilp1 ) and Z band alternatively spliced PDZ-motif protein 67 ( Zasp67 ). The tblastn search of D. melanogaster Ilp4-PA (query) against the D. eugracilis (GenBank Accession: GCA_000236325.2) Genome Assembly (database) placed the putative ortholog of Ilp4 within scaffold scf7180000409711 (KB465257.1) at locus LOC108114483 (XP_017080990.1)— with an E-value of 8e-23 and a percent identity of 43.94%. Furthermore, the putative ortholog nested within LOC108114479 (XP_017080986.1) alongside LOC108114482 (XP_017080989.1), LOC108113894 (XP_017080088.1), and LOC108114481 (XP_017080988.1), which correspond to CG32052, Ilp3, CG33483 , and Ilp2 in D. melanogaster (E-value: 0.0, 2e-48, 1e-68, and 3e-53; identity: 91.26%, 68.63%, 57.40%, and 59.71%, respectively, as determined by blastp ; Figure 1A , Altschul et al., 1990 ). The putative ortholog of Ilp4 is flanked upstream by LOC108114394 (XP_017080854.1), LOC108114226 (XP_017080582.1), and LOC108114228 (XP_017080583.1) which is nested by LOC108114224 (XP_017080567.1), which correspond to Cdk8, I-2, Ilp5 , and CG43897 in D. melanogaster (E-value: 0.0, 1e-100, 2e-38, and 0.0; identity: 97.14%, 85.37%, 56.25%, and 80.83%, respectively, as determined by blastp ). The putative ortholog of Ilp4 is flanked downstream by LOC108114480 (XP_017080987.1) and LOC108114478 (XP_017080982.1), which correspond to Ilp1 and Zasp67 in D. melanogaster (E-value: 3e-59 and 0.0; identity: 63.64% and 82.66%, respectively, as determined by blastp ). The putative ortholog assignment for Ilp4 in D. eugracilis is supported by the following evidence: The genes surrounding the Ilp4 ortholog are orthologous to the genes at the same locus in D. melanogaster and synteny is completely conserved, supported by e-values and percent identities, so we conclude that LOC108114483 is the correct ortholog of Ilp4 in D. eugracilis ( Figure 1A ). Download figure Open in new tab Figure 1: Ilp4 gene model comparison between Drosophila eugracilis and Drosophila melanogaster. (A) Synteny comparison of the genomic neighborhoods for Ilp4 in Drosophila melanogaster and D. eugracilis . Thin underlying arrows indicate the DNA strand within which the target gene– Ilp4 –is located in D. melanogaster (top) and D. eugracilis (bottom). The thin arrows pointing to the left indicate that Ilp4 is on the negative (-) strand in D. eugracilis and D. melanogaster . The wide gene arrows pointing in the same direction as Ilp4 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Ilp4 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. eugracilis indicate orthology to the corresponding gene in D. melanogaster , while grey gene arrows indicate a gene insertion in D. eugracilis . Gene symbols given in the D. eugracilis gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. eugracilis . (B) Gene Model in GEP UCSC Track Data Hub (Raney et al ., 2014) . The coding-regions of Ilp4 in D. eugracilis are displayed in the User Supplied Track (black); coding exons are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. eugracilis ), Spaln of D. melanogaster Proteins (light purple, alignment of Ref-Seq proteins from D. melanogaster ), RNA-Seq from Adult Females and Mixed Embryos (red and dark purple, respectively; alignment of Illumina RNA-Seq reads from D. eugracilis ), and Splice Junctions Predicted by regtools using D. eugracilis RNA-Seq (PRJNA63469). The splice junction which aligns with Ilp4 (JUNC00079282) has a read-depth of 657. (C) Dot Plot of Ilp4-PA in D. melanogaster ( x -axis) vs. the orthologous peptide in D. eugracilis ( y -axis) . Amino acid number is indicated along the left and bottom; coding-exon number is indicated along the top and right, and exons are also highlighted with alternating colors. The black diagonal lines indicate sequence similarity and are highlighted by the green box denoted I and the purple box denoted II. (D) Protein alignment between D. melanogaster Ilp4-PA and its putative ortholog in D. eugracilis . The alternating colored rectangles represent adjacent exons. The symbols in the match line denote the level of similarity between the aligned residues. An asterisk ( * ) indicates that the aligned residues are identical. A colon (:) indicates the aligned residues have highly similar chemical properties—roughly equivalent to scoring > 0.5 in the Gonnet PAM 250 matrix ( Gonnet et al., 1992 ). A period (.) indicates that the aligned residues have weakly similar chemically properties—roughly equivalent to scoring > 0 and ≤ 0.5 in the Gonnet PAM 250 matrix. A space indicates a gap or mismatch when the aligned residues have a complete lack of similarity—roughly equivalent to scoring ≤ 0 in the Gonnet PAM 250 matrix. The green box denoted I and the purple boxes denoted II correspond to the boxes in figure 1C, respectively. Protein Model Ilp4 in D. eugracilis has one protein-coding isoform (Ilp4-PA; Figure 1B ). Isoform (Ilp4-PA) contains two protein-coding exons. Relative to the ortholog in D. melanogaster , the coding-exon number and isoform count are conserved. The sequence of Ilp4-PA in D. eugracilis has 60.00% identity (E-value: 1e-38) with the protein-coding isoform Ilp4-PA in D. melanogaster , as determined by blastp ( Figure 1C ). Unusual characteristics of this model include the low sequence similarity across the end of protein-coding exon one and beginning of protein-coding exon two, spanning the region in between green box I and purple box(es) II ( Figures 1C, 1D ). RNA-Seq Data The RNA-Seq data supported the final reconciled model. Peaks in the data correspond to exons while low coverage areas indicate introns. There was no RNA-Seq data for adult males, and the embryonic data reports higher reads than the adult female track which has very low coverage. Brogiolo et al . found that Ilp4 is highly expressed in embryonic mesoderm and midgut, and the RNA-Seq data supports the higher expression of Ilp4 in Drosophila embryos. Any RNA-Seq reads that extend past the 5’ and 3’ ends of the model can be attributed to untranslated regions and to the nesting gene. 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. melanogaste r reference gene. Coordinates of CDSs are then refined by examining aligned modENCODE RNA-Seq data, and by applying paradigms of molecular biology such as identifying canonical splice site sequences and ensuring the maintenance of an open reading frame across hypothesized splice sites. Students then confirm the biological validity of their target gene model using the Gene Model Checker ( https://gander.wustl.edu/~wilson/dmelgenerecord/index.html ; Rele et al., 2023 ), which compares the structure and translated sequence from their hypothesized target gene model against the D. melanogaster reference gene model. At least two independent models for a gene are generated by students under mentorship of their faculty course instructors. Those models are then reconciled by a third independent researcher mentored by the project leaders to produce the final model. Note: comparison of 5’ and 3’ UTR sequence information is not included in this GEP CURE protocol.” ( Gruys et al, 2025 ) Supplemental Material Zip file containing FASTA, PEP, GFF files for the gene model Figure 1 in high resolution Metadata Bioinformatics, Genomics, Drosophila , Genotype Data, New Finding Funding This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/ ; PI-Laura K. Reed). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health. Acknowledgements We thank Wilson Leung (Washington University, St. Louis) for developing and maintaining the technological infrastructure that supported the creation of this gene model, as well as Chinmay Rele and Laura K. Reed (University of Alabama) for their guidance and encouragement throughout the project. We are also grateful to FlyBase for providing the authoritative 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. Funder Information Declared National Science Foundation , 1915544 National Institute of General Medical Sciences of the National Institutes of Health , R25GM130517 References ↵ Altschul , S.F. , Gish , W. , Miller , W. , Myers , E.W. & Lipman , D.J. ( 1990 ) “Basic local alignment search tool.” J . Mol. Biol . 215 : 403 – 410 . PMID: 2231712 OpenUrl CrossRef PubMed Web of Science Baker RH , DeSalle R. 1997 . Multiple sources of character information and the phylogeny of Hawaiian drosophilids . Systems Biology 46 ( 4 ): 654 – 73 . OpenUrl Biglou , S.G. , W.G. Bendena , and I. Chin-Sang , An overview of the insulin signaling pathway in model organisms Drosophila melanogaster and Caenorhabditis elegans . Peptides , 2021 . 145 : p. 170640 . PMID: 34450203 OpenUrl CrossRef PubMed ↵ Bock , I. R. , & Wheeler , M. R. ( 1972 ). The Drosophila melanogaster species group . University of Texas Publications , 7213 , 1 – 102 . OpenUrl ↵ Brogiolo , W. , Stocker , H. , Ikeya , T. , Rintelen , F. , Fernandez , R. and Hafen , E. , 2001 . An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control . Current Biology 11 , 213 – 221 . PMID: 11250149 OpenUrl CrossRef PubMed Web of Science Carson HL . 1983 . Chromosomal sequences and interisland colonizations in hawaiian Drosophila . Genetics 103 ( 3 ): 465 – 82 . OpenUrl Abstract / FREE Full Text Carson HL , Hardy DE , Spieth HT , Stone WS . 1970 . The Evolutionary Biology of the Hawaiian Drosophilidae . Essays in Evolution and Genetics in Honor of Theodosius Dobzhansky : 437 – 543 ↵ Chen , Z.X. , Sturgill , D. , Qu , J. , Jiang , H. , Park , S. , Boley , N. , Suzuki , A.M. , Fletcher , A.R. , Plachetzki , D.C. , FitzGerald , P.C. , Artieri , C.G. , Atallah , J. , et al. , 2014 . Comparative validation of the D. melanogaster modENCODE transcriptome annotation . Genome Res ., 24 ( 7 ): 1209 – 23 . PMID: 24985915 OpenUrl Abstract / FREE Full Text Drosophila 12 Genomes Consortium , Clark , A. G. , Eisen , M. B. , Smith , D. R. , Bergman , C. M. , Oliver , B. , Markow , T. A. , Kaufman , T. C. , Kellis , M. , Gelbart , W. , Iyer , V. N. , Pollard , D. A. , Sackton , T. B. , Larracuente , A. M. , Singh , N. D. , Abad , J. P. , Abt , D. N. , Adryan , B. , Aguade , M. , … MacCallum , I. ( 2007 ). Evolution of genes and genomes on the Drosophila phylogeny . Nature , 450 ( 7167 ), 203 – 218 . doi: 10.1038/nature06341 . PMID: 17994087 OpenUrl CrossRef PubMed Web of Science ↵ Duda , O. ( 1924 ). Revision der europäischen und grönländischen sowie einiger südostasiatischen Arten der Gattung Piophila Fallén (Dipteren) . Konowia , 3 , 97 – 113 . OpenUrl ↵ Gonnet , G.H. , Cohen , M.A. and Benner , S.A. , 1992 . Exhaustive matching of the entire protein sequence database . Science 256 , 1443 . PMID: 1604319 OpenUrl Abstract / FREE Full Text Grönke , S. , Clarke , D.-F. , Broughton , S. , Andrews , T.D. and Partridge , L. , 2010 . Molecular Evolution and Functional Characterization of Drosophila Insulin-Like Peptides . PLOS Genetics 6 , e1000857 . PMID: 20195512 OpenUrl CrossRef PubMed ↵ 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 . 025 :10.17912/micropub.biology.001168. eCollection 2025. doi: 10.17912/micropub.biology.001168 . PMID: 39845267 . OpenUrl CrossRef PubMed Guirao-Rico , S. and Aguadé , M. , 2011 . Molecular Evolution of the Ligands of the Insulin-Signaling Pathway: dilp Genes in the Genus Drosophila . Molecular Biology and Evolution 28 , 1557 – 1560 . PMID: 21196470 OpenUrl CrossRef PubMed Web of Science Kambysellis MP , Ho KF , Craddock EM , Piano F , Parisi M , Cohen J. 1995 . Pattern of ecological shifts in the diversification of Hawaiian Drosophila inferred from a molecular phylogeny . Current Biology 5 ( 10 ): 1129 – 39 . OpenUrl CrossRef PubMed Web of Science Kaneshiro , KY , RG Gillespie , and HL Carson . “ Chromosomes and male genitalia of Hawaiian Drosophila: tools for interpreting phylogeny and geography .” Hawaiian biogeography: evolution on a hot spot archipelago ( 1995 ): 57 – 71 Kent WJ , Sugnet CW , Furey TS , Roskin KM , Pringle TH , Zahler AM , Haussler D. 2002 . TheHuman Genome Browser at UCSC . Genome Res . 12 : 996 – 1006 . DOI: 10.1101/gr.229102 OpenUrl Abstract / FREE Full Text ↵ Mudge JM , Harrow J. 2016 . The state of play in higher eukaryote gene annotation . Nat Rev Genet 17 : 758 – 772 . DOI: 10.1038/nrg.2016.119 OpenUrl CrossRef PubMed ↵ Morgan , A. , Kiser , C. A. , Bronson , I. , Lin , H. , Guillette , N. , McMahon , R. , Kennell , J. A. , Long , L. J. , Reed , L. K. , & Rele , C. P. ( 2022 ). Drosophila eugracilis – Akt. microPublication Biology, eCollection 2022 . doi: 10.17912/micropub.biology.000544 OpenUrl CrossRef PubMed ↵ Myers A , Hoffman A , Natysin M , Arsham AM , Stamm J , Thompson JS , Rele CP , Reed LK . Gene model for the ortholog Myc in Drosophila ananassae . 2024 . MicroPubl Biol . DOI: 10.17912/micropub.biology.000856 OpenUrl CrossRef PubMed ↵ Navarro Gonzalez J , Zweig AS , Speir , ML , Schmelter D , Rosenbloom KR , Raney BJ , et al. , 2021 . The UCSC Genome Browser database: 2021 update . Nucl Acids Res 49 : 1046 – 1057 . DOI: 10.1093/nar/gkaa107 OpenUrl CrossRef PubMed ↵ Newell , N.R. , Ray , S. , Dalton , J.E. , Fortier , J.C. , Kao , J.Y. , Chang , P.L. , Nuzhdin , S.V. and Arbeitman , M.N. , 2020 . The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions . G3 (Bethesda, Md .) 10 , 967 – 983 . PMID: 31907222 OpenUrl Abstract / FREE Full Text Oldenberg , L. 1914 . Beitrag zur Kenntnis der europäische n Drosophiliden (Dipt .). Archiv für Naturgeschichte (A) 80 ( 2 ): 1 - 42 . [1914.05.18] OpenUrl ↵ Pélandakis , M. , Higgins , D. G. , & Solignac , M. ( 1993 ). Molecular phylogeny of the Drosophila melanogaster species subgroup: A comparison of mitochondrial and nuclear genes . Journal of Molecular Evolution , 37 ( 6 ), 525 – 543 . doi: 10.1007/BF00178867 OpenUrl CrossRef PubMed Web of Science Raney , B. J. , Dreszer , T. R. , Barber , G. P. , Clawson , H. , Fujita , P. A. , Wang , T. , … & Kent , W. J. ( 2014 ). Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser . Bioinformatics , 30 ( 7 ), 1003 – 1005 . doi: 10.1093/bioinformatics/btt637 OpenUrl CrossRef PubMed Web of Science ↵ Rele CP , Sandlin KM , Leung W , Reed LK . 2023 . Manual annotation of Drosophila genes: a Genomics Education Partnership protocol . F1000Research 11 : 1579 . DOI: 10.12688/f1000research.126839.2 OpenUrl CrossRef ↵ Tello-Ruiz MK , Marco CF , Hsu FM , Khangura RS , Qiao P , Sapkota S , et al. 2019 . Double triage to identify poorly annotated genes in maize: The missing link in community curation . PLoS One 14 : e0224086 . DOI: 10.1371/journal.pone.0224086 OpenUrl CrossRef PubMed ↵ Wigby , S. , Slack , C. , Grönke , S. , Martinez , P. , Calboli , F.C.F. , Chapman , T. and Partridge , L. , 2011 . Insulin signalling regulates remating in female Drosophila . Proceedings. Biological sciences 278 , 424 – 431 . PMID: 20739318 OpenUrl CrossRef PubMed ↵ Wu , Q. and Brown , M.R. , 2005 . Signaling and function of insulin-like peptides in insects . Annual Review of Entomology 51 , 1 – 24 . PMID: 16332201 OpenUrl PubMed View the discussion thread. Back to top Previous Next Posted September 08, 2025. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Gene model for the ortholog of Ilp4 in Drosophila eugracilis Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Gene model for the ortholog of Ilp4 in Drosophila eugracilis Rachael Cowan , Amun Uppal , Clairine I. S. Larsen , Christopher E. Ellison , Nicole S. Torosin , Jeffrey S. Thompson , Chinmay P. Rele , Lori Boies bioRxiv 2025.09.05.674564; doi: https://doi.org/10.1101/2025.09.05.674564 Share This Article: Copy Citation Tools Gene model for the ortholog of Ilp4 in Drosophila eugracilis Rachael Cowan , Amun Uppal , Clairine I. S. Larsen , Christopher E. Ellison , Nicole S. Torosin , Jeffrey S. Thompson , Chinmay P. 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