microPublication Biology 2578-9430 Caltech Library 10.17912/micropub.biology.002318 new finding gene model drosophila Gene model for the ortholog of dib in Drosophila cardini Brooks Parker Data curation Formal analysis Investigation Writing - review & editing 1 Chialvo Pablo Investigation Formal analysis Writing - review & editing Validation 1 Scott Chialvo Clare Conceptualization Supervision Validation Writing - original draft 1 § Biology, Appalachian State University, Boone, North Carolina USA Findlay Geoff Correspondence to: Clare Scott Chialvo ( chialvoch@appstate.edu )

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

 31 7 2026 2026 2026 10.17912/micropub.biology.002318 17 7 2026 27 7 2026 30 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.

We developed a gene model for the disembodied ortholog ( dib ) in the ASM1890373v1 Genome Assembly (GenBank Accession: GCA_018903735.1 ) of Drosophila cardini . This ortholog was characterized as part of a developing dataset for a comparative study of detoxification gene family evolution in the immigrans - tripunctata radiation of the genus Drosophila using an adapted Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

This gene annotation project was funded by Nation Science Foundation grants DEB-1737869 (PI LKR, CoPI CSC) and DBI-2217912 (PI CSC). The Genomics Education Partnership (GEP; https://thegep.org/ ), which supports this project, is funded by the National Science Foundation (1915544; PI LKR) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517; PI LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.

(A) Synteny comparison of the genomic neighborhoods for dib in Drosophila melanogaster and D. cardini . Thin underlying arrows indicate which DNA strand the target gene, dib , is located on in D. melanogaster (top) and D. cardini (bottom). The thin arrows pointing to the right indicate that dib is on the positive strand in both D. melanogaster and D. cardini . The wide gene arrows pointing in the same direction as dib are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of dib are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. cardini indicate orthology to the corresponding gene in D. melanogaster . Gene symbols given in the D. cardini gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. cardini . (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of dib in D. cardini are displayed in the User Supplied Track (red); coding sequences (CDS) are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster ), Coding Regions Predicted by Augustus (dark blue), GeMoMa (teal), and NSCAN PASA-EST (dark green), and RNA-Seq from mixed sex adult flies (brown; alignment of Illumina RNA-Seq reads from D. cardini – Erlenbach et al. 2023). (C) Dot Plot of dib-PA in D. melanogaster ( x -axis) vs. the orthologous peptide in D. cardini ( y -axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. Line breaks in the dot plot indicate areas of amino acid mismatch between species. We do not note any significant breaks.

Description

Introduction

This article reports a predicted gene model generated by undergraduate work using a structured gene model annotation protocol defined by the Genomics Education Partnership (GEP; thegep.org) for Course-based Undergraduate Research Experience (CURE). The following information in quotes may be repeated in other articles submitted by participants using the same GEP CURE protocol for annotating Drosophila species orthologs of Drosophila melanogaster detoxification genes.

“Within insects, detoxifying xenobiotics and host secondary metabolites is a three-phase process that involves functionalization, conjugation, and excretion of these compounds. Expansions of known detoxification gene families ( e.g. , cytochrome P450s) are associated with diet breadth and insecticide resistance (Ranson et al., 2002; Després et al., 2007; Rane et al., 2016). With the increasing availability of high-quality genomes for non-model organisms, including Drosophila species beyond D. melanogaster , it is now possible to perform large scale comparative studies (Robinson et al., 2011; Kim et al., 2021; Threfall and Baxter 2021). Careful manual annotation and curation of gene models can improve upon computational gene predictions in non-model species, which aids the accuracy of studies on gene and genome evolution (Mudge and Harrow 2016; Tello-Ruiz et al., 2019). To aid in these annotations, the Genomics Education Partnership (thegep.org) developed a curriculum involving web-based tools that allow undergraduates to engage in authentic course-based research focused on manually annotating genes in non-model species (Rele et al., 2023). The orthologous gene models, including the one presented here, then provide a reliable basis for further evolutionary genomic analyses when made available to the scientific community. The gene ortholog described here in D. cardini for disembodied ( dib ), a member of the cytochrome P450 monooxygenase gene family, was characterized as part of a developing dataset for a comparative study of detoxification gene families in the immigrans - tripunctata radiation of the genus Drosophila .” (Williams et al, 2026) 

“In the subgenus Drosophila , D. cardini Sturtevant 1916 is a member of the cardini subgroup in the cardini species group of the immigrans-tripunctata radiation (Heed & Krishnamurthy 1959; Bächli 2005). Species in the cardini subgroup are found in the mainland Neotropics, and the range of D. cardini extends from Florida to Brazil (Heed, 1962). Members of the cardini group primarily feed and develop on fruit and flowers (Markow & O'Grady 2008). However, D. cardini is also reported to feed on mushrooms and can tolerate the cyclopeptide toxin α-amanitin (Stump et al. 2011).” (Patel et al., 2026)

“Cytochrome P450 monooxygenases (CYPs) are a family of phase I detoxification enzymes that are found in almost all aerobic organisms and act by oxidizing compounds to make them more polar (Stegeman and Livingstone, 1998; Li et al., 2007). The enzymes in this family vary in both their substrate specificity and the range of metabolites that they produce (Rendic and Di Carlo 1997; Scott 1999). Furthermore, the substrate specificity of CYPs can be altered by a change in a single amino acid (Lindberg and Negishi, 1989).” (Patel et al., 2026)

disembodied ( dib ), a mitochondrial CYP whose expression is restricted to the prothoracic gland, is a member of the Halloween gene group (Gilbert 2004). These genes act in the biosynthetic pathway that produces 20-Hydroxyecdysone, a hormone that controls metamorphosis and development in arthropods (Gilbert and Warren 2005; Rewitz et al., 2006). Homozygous dib mutants die prior to completing embryogenesis and display abnormal cuticular development (Warren et al. 2002; Gilbert 2004).

We propose a gene model for the D. cardini ortholog of the D. melanogaster disembodied ( dib ) gene. The genomic region of the ortholog corresponds to the Augustus gene prediction JAEIGM010000007.g432.t1 in the ASM1890373v1 Genome Assembly of D. cardini ( GCA_018903735.1 – Kim et al., 2021). This model is based on the mixed sex adult RNA-Seq data from D. cardini (Erlenbach et al., 2023; https://doi.org/10.5061/dryad.hdr7sqvq2) and dib  in D. melanogaster using FlyBase release FB2024_02 ( GCA_000001215.4 ; Gramates et al., 2022; Jenkins et al., 2022; Larkin et al., 2021).

Synteny

The reference gene, dib, occurs on chromosome 3L in D. melanogaster and is flanked upstream by UDP-glycosyltransferase family 305 member A1 ( Ugt305A1 ), CG1136 , and Dpy-30-like 2 ( Dpy-30L2 ) which is nested in CG1136 and downstream by wishful thinking ( wit ), CG32259 (which is nested in wit ), and Fumarylacetoacetase ( Faa ). The tblastn search of D. melanogaster dib-PA (query) against the D. cardini genome assembly (GenBank Accession: GCA_018903735.1 ; subject) placed the putative ortholog of dib within contig_2202 (JAEIGM010000007.1) which corresponds to Augustus gene prediction JAEIGM010000007.g432.t1 (E-value: 0.0; percent identity: 79.75% as determined by blastp ). The putative ortholog is flanked upstream by the Augustus gene predictions JAEIGM010000007.g431.t1 and JAEIGM010000007.g429.t1, which correspond to UGt305A1 and CG1136 in D. melanogaster (E-value: 5e-160 and 0.0; identity: 45.3% and 65.92%, respectively, as determined by blastp ; Figure 1A ; Altschul et al., 1990). Augustus gene prediction JAEIGM010000007.g430.t1 did not map to gene expression data and was not included. The putative ortholog of dib is flanked downstream by the Augustus gene predictions JAEIGM010000007.g433.t1 and JAEIGM010000007.g434.t1, which correspond to wit and Faa in D. melanogaster (E-value: 0.0 and 0.0; identity: 74.81% and 87.77%, respectively, as determined by blastp ). The putative ortholog assignment for dib in D. cardini is supported by the following evidence: The gene predictions surrounding the dib ortholog are orthologous to the genes at the same locus in D. melanogaster , gene expression data corresponds with each prediction, and local synteny is completely conserved, supported by E-values and percent identities, so we conclude that the Augustus prediction JAEIGM010000007.g432.t1 represents an ortholog of dib in D. cardini ( Figure 1A ).

Protein Model

dib in D. cardini has 4 coding sequences (CDS) within its genomic DNA sequence. The only unique protein sequence (dib-PA) is translated from 1 mRNA isoform (dib-RA; Figure 1B ). Relative to the ortholog in D. melanogaster , the CDS number and protein isoform count are conserved . The sequence of dib-PA in D. cardini has 79.4% identity (91.0% similarity) with the protein-coding isoform dib-PA in D. melanogaster , as determined by blastp ( Figure 1C ). This level of divergence is not surprising given that D. cardini and D. melanogaster belong to two separate subgenera ( Drosophila and Sophophora respectively) that diverged approximately 45-60 MYA (Russo et al., 1995; Tamura et al. 2004; Obbard et al., 2012). Coordinates of this curated gene model are archived in the CaltechDATA repository (see “Extended Data” section below).

Methods

The annotation methods used in this project are adapted from those described in Rele et al. (2023), which includes algorithms, database versions, and citations for the complete annotation process developed for the Pathways Project. The methods for the current project are detailed in brief below with notes on significant differences between this protocol and the one described in Rele et al. (2023). The students use the GEP instance of the UCSC Genome Browser v.435 (https://gander.wustl.edu ; Kent WJ et al., 2002; Raney et al., 2024) to examine the genomic neighborhood of their reference detoxification gene in the D. melanogaster genome assembly (Aug. 2014; BDGP Release 6 + ISO1 MT/dm6). Students obtain the protein sequence for the D. melanogaster target gene for a given isoform and use a tblastn search of the sequence against their target Drosophila species genome assembly ( D. cardini (GCA_018903735.1 - Kim et al., 2021)) on the NCBI BLAST server (https://blast.ncbi.nlm.nih.gov/Blast.cgi, Altschul et al., 1990) to identify the putative ortholog location. Students compare the genomic neighborhood of the putative ortholog to that of the reference gene in D. melanogaster . This local synteny analysis includes a minimum of two upstream and two downstream genes relative to the potential ortholog. As no RefSeq protein data is available for these species, comparisons are based on gene predictions that correlate with gene expression data in the putative ortholog neighborhood. Using the multiple alignment tracks feature in the Genome Browser, students examine other sets of genomic evidence, including Spaln alignment of D. melanogaster proteins, multiple gene prediction tracks (e.g., GeMoMa, Augustus, NSCAN PASA-EST), and RNA-Seq mixed seq adult expression data from the target species generated by Erlenbach et al. (2023; https://doi.org/10.5061/dryad.hdr7sqvq2). Information on the genomic structure information (e.g., CDSs, intron-exon number, number of isoforms) for the reference gene in D. melanogaster is retrieved using Gene Record Finder (https://gander.wustl.edu/~wilson/dmelgenerecord/index.html; Rele et al ., 2023). To determine approximate splice sites within the target gene, a tblastn search using the CDSs from the D. melanogaste r reference gene against the putative ortholog location (10kb up- and downstream of the target gene prediction). Coordinates of the CDS(s) are refined by examining aligned RNA-Seq data, identifying canonical splice site sequences, and ensuring the maintenance of an open reading frame. Students confirm the biological validity of their target gene model using the FlySeq Gene Model Checker (https://gander2.wustl.edu/~wilson/genechecker-flyseq/), which compares the hypothesized target gene model's structure and translated sequence against the D. melanogaster reference gene. At least two independent models for this gene are generated. These models are reconciled by a third independent researcher to produce the final model presented here. Note: comparison of 5' and 3' UTR sequence information is not included in this GEP CURE protocol.

Extended Data

Description: Zipped archive containing FASTA, PEP, and GFF files for dib model. Resource Type: Dataset. DOI: https://doi.org/10.22002/pm412-0xx64

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model and Laura K. Reed for overseeing the Genomics Education Partnership. Thank you to FlyBase for providing the definitive database for Drosophila melanogaster gene models.

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