microPublication Biology 2578-9430 Caltech Library 10.17912/micropub.biology.001031 new finding genotype data drosophila Gene model for the ortholog of gig in Drosophila ananassae Backlund Anne E. Formal analysis Validation Writing - original draft Writing - review & editing 1 Cohen Logan Data curation Validation Visualization Writing - review & editing 2 Sileo Gregory Formal analysis Writing - review & editing 3 Alberts Ian Formal analysis Writing - review & editing 4 Giarla Thomas C. Supervision Writing - review & editing 3 Rele Chinmay P. Data curation Formal analysis Methodology Project administration Software Supervision Validation Visualization Writing - review & editing 1 Reed Laura K. Conceptualization Methodology Resources Validation Writing - review & editing 1 § The University of Alabama, Tuscaloosa, AL USA Worcester State University, Worcester MA, USA Siena College, Loudonville, NY USA University of Evansville, Evansville IN USA Correspondence to: Laura K. Reed ( lreed1@ua.edu )

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

 6 7 2026 2026 2026 10.17912/micropub.biology.001031 12 10 2023 26 6 2026 3 7 2026 Copyright: © 2026 by the authors 2026 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Gene model for the ortholog of gigas ( gig ) in the D. ananassae May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ). 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.

National Science Foundation (United States) https://ror.org/021nxhr62 1915544 LK Reed National Institutes of Health (United States) https://ror.org/01cwqze88 R25GM130517 LK Reed This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (GEP; https://thegep.org/; PI-LKR). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health nor the National Science Foundation.

(A) Synteny comparison of the genomic neighborhoods for gig in Drosophila melanogaster and D. ananassae . Thin underlying arrows indicate the DNA strand within which the target gene— gig —is located in D. melanogaster (top) and D. ananassae (bottom). The thin arrows pointing to the right indicate that gig is on the positive (+) strand in D. ananassae and D. melanogaster . The wide gene arrows pointing in the same direction as gig are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of gig are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. ananassae indicate orthology to the corresponding gene in D. melanogaster , while black gene arrows indicate non-orthology. Gene symbols 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 GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of gig in D. ananassae are displayed in the User Supplied Track (black); coding CDSs are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. ananassae ), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster ), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females, Adult Males, and Wolbachia cured Embryos (red, light blue, and pink, respectively; alignment of Illumina RNA-Seq reads from D. ananassae ), and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq ( SRP006203 , SRP007906 , PRJNA257286 , PRJNA388952 ). Splice junctions shown have read-depths of 100-499 and 500-999 supporting reads in pink or brown, respectively. (C) Dot Plot of gig-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. Line breaks in the dot plot indicate mismatching amino acids at the specified location between species. (D) Tenth CDS of Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The same evidence tracks as Figure 1B are displayed, in addition to the TBLASTN Mapping of D. melanogaster CDS track. Isoforms gig-RA and gig-RB differ only by the length of the tenth coding CDS: gig-RB is slightly shorter than gig-RA . Although there is only one prediction in the BLAT Alignment of NCBI RefSeq Genes track, the presence of the splice acceptor (AG) in the conserved position (red box) suggests that isoform gig-RB also exists in D. ananassae .

Description

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).

“Gene gig (short for gigas, aka TSC2 , CG697 5, FBgn0005198) encodes a tumor suppressor protein that controls cell size, cell proliferation, and organ size (Ito and Rubin 1999). The gig protein contains a GTPase-activating protein (GAP) domain and forms a complex with protein Tsc1 (Gao et al., 2001; Potter et al., 2001). The gig-Tsc1 protein complex promotes GTP hydrolysis of the small G-protein Rheb (Ras homolog enriched in brain), thereby antagonizing the insulin and TOR signaling pathways (Gao et al., 2002; Zhang et al., 2003). This gene was originally identified in humans as TSC2, and mutations in TSC1 or TSC2 result in tuberous sclerosis, a syndrome characterized by widespread benign tumors (European Consortium 1993; van Slegtenhorst et al., 1997).” (Gruys et al., 2025b).

“ 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).

We propose a gene model for the D. ananassae ortholog of the D. melanogaster gigas ( gig ) gene. The genomic region of the ortholog corresponds to the uncharacterized protein XP_001956634.1 (Locus ID LOC6507933 ) in the May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly of D. ananassae ( GCA_000005115.1 ; Drosophila 12 Genomes Consortium et al., 2007). This model is based on RNA-Seq data from D. ananassae ( SRP006203 , SRP007906 , PRJNA257286 , PRJNA388952 ; Graveley et al., 2011) and gig in D. melanogaster using FlyBase release FB2023_03 ( GCA_000001215.4 ; Larkin et al., 2021; Gramates et al., 2022).

Synteny

The reference gene, gig, occurs on chromosome 3L in D. melanogaster and is flanked upstream by CG14187 and CG7365 and downstream by CG7328 and CG42674 . The genes obstructor-J ( obst-J ) and CG7335 are nested within gig , and Snakeskin ( Ssk ) is nested within CG42674 . The tblastn search of D. melanogaster gig-PA (query) against the D. ananassae (GCA000005115.1) Genome Assembly (database) placed the putative ortholog of gig within scaffold_13337 at locus LOC6507933 ( XP_001956634.1 )— with an E-value of 0.0 and a percent identity of 68.20%. Furthermore, the putative ortholog is flanked upstream by LOC6507122 ( XP_001956632.1 ) and LOC6507121 ( XP_044570979.1 ), which correspond to Grip163 and endos ulfine ( endos ) in D. melanogaster (E-value: 0.0 and 3e-83; identity: 54.05% and 97.48%, respectively, as determined by blastp ; Figure 1A ; Altschul et al., 1990). The putative ortholog of gig is flanked downstream by LOC6507118 ( XP_001956637.1 ) and LOC6507117 ( XP_032310418.1 ), which correspond to CG7328 and CG42674 in D. melanogaster (E-value: 1e-161 and 0.0; identity: 68.54% and 82.06%, respectively, as determined by blastp ). LOC6507120 ( XP_001956635.1 ) and LOC6507119 ( XP_001956636.1 ) are nested within gig (E-value: 1e-143 and 2e-170; identity: 53.95% and 65.33%). LOC6507934 ( XP_001956640.1 ) is nested within CG42674 (E-value: 8e-115, identity: 98.77%). The putative ortholog assignment for gig in D. ananassae is supported by the following evidence: The genes downstream of and nested within the gig ortholog are orthologous to the genes at the same locus in D. melanogaster and local synteny is mostly conserved, supported by results generated from blastp , so we conclude that LOC6507933 is the correct ortholog of gig in D. ananassae ( Figure 1A ).

Protein Model

gig in D. melanogaster has two protein-coding isoforms (gig-PA and gig-PB; Figure 1B ). Both mRNA isoforms contain fifteen protein-coding CDSs, but gig-RB has a slightly shorter tenth CDS than gig-RA . The isoform and protein-coding CDS counts are conserved in D. ananassae . The sequence of gig-PA in D. ananassae has 87.67% identity (E-value: 0.0) with the protein-coding isoform gig-PA in D. melanogaster , as determined by blastp ( Figure 1C ). Coordinates of this curated gene model (gig-PB, gig-PA) are stored by NCBI at GenBank/BankIt (accession BK064615 , BK064616 , respectively). These data are also archived in the CaltechDATA repository (see “Extended Data” section below).

Special characteristics of the protein model

Although there is only one prediction in the BLAT Alignment of NCBI RefSeq Genes track ( Figure 1B ), there is evidence that both isoforms of gig are present in D. ananassae . gig-RA and gig-RB differ only by the length of their tenth CDS: gig-RB 's CDS is slightly shorter than gig-RA . There is a splice acceptor site (AG) in the same reading frame that gig-RA uses ( Figure 1D ), which suggests that isoform gig-RB exists in D. ananassae . The TBLASTN Mapping of D. melanogaster CDS track also supports the presence of gig-RB .

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/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., 2025a).

Extended Data

Description: Zip file containing FASTA, PEP, and GFF of the model. Resource Type: Model. DOI: https://doi.org/10.22002/am768-qep80

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 for assistance in updating the manuscript to the current template.

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