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. 2025 Sep 11;2025:10.17912/micropub.biology.001848. doi: 10.17912/micropub.biology.001848

Gene model for the ortholog of dock in Drosophila eugracilis

Gabriella N Bicanovsky 1, Megan E Lawson 1, Alexandria Groeneveld 2, Jordan Elkinton 3, Eden Dowell 3, S F Shelley-Tremblay 1, Stephanie Toering Peters 4, Lindsey J Long 3, Anya Goodman 5, Melinda A Yang 6, Chinmay P Rele 1, Laura K Reed 1,§
Reviewed by: Christopher Shaffer
PMCID: PMC12464739  PMID: 41018033

Abstract

Gene model for the ortholog of dreadlocks ( dock ) in the D. eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0) (DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2 ) of Drosophila eugracilis . 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.

Figure 1. Genomic neighborhood and gene model for dock in Drosophila eugracilis .

Figure 1. Genomic neighborhood and gene model for dock in Drosophila eugracilis

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(A) Synteny of genomic neighborhood of dock in D. melanogaster and D. eugracilis . Gene arrows pointing in the same direction as target gene in both D. eugracilis and D. melanogaster are on the same strand as the target gene; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that dock is on the + strand. White arrows in D. eugracilis indicate the locus ID and the orthology to the corresponding gene in D. melanogaster . The gene names 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 UCSC Track Hub (Raney et al., 2014): the gene model in D. eugracilis (black), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster ), BLAT alignments of NCBI Ref-Seq Genes (blue, alignment of Ref-Seq genes for D. eugracilis ), RNA-Seq from adult females (red), adult males (blue), and mixed embryos (purple), alignment of Illumina RNA-Seq reads from D. eugracilis , and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. eugracilis RNA-Seq (PRJNA63469). Splice junctions shown have a minimum read-depth of 105 with 100-499 and 500-999 supporting reads in pink and brown, respectively. 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 dock-PB 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 (CDS) number is indicated along the top and right, and CDSs are also highlighted with alternating colors.

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).

“ D. eugracilis (NCBI:txid29029) is part of the melanogaste r 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 (https://www.taxodros.uzh.ch, accessed 1 Feb 2023).” (Morgan et al., 2022).

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We propose a gene model for the D. eugracilis ortholog of the D. melanogaster dreadlocks ( dock ) gene. The genomic region of the ortholog corresponds to the uncharacterized protein XP_017075680.1 (Locus ID LOC108110918 ) in the Apr. 2013 (BCM-HGSC.DEUG_2.0) Genome Assembly of D. eugracilis ( GCA_000236325.2 ). This model is based on RNA-Seq data from D. eugracilis ( PRJNA63469 ; Chen et al., 2014) and dock in D. melanogaster using FlyBase release FB2023_03 ( GCA_000001215.4 ; Larkin et al., 2021; Gramates et al., 2022; Jenkins et al., 2022).

The product of gene dreadlocks ( dock , FBgn0010583) is involved in several cellular functions, including axon guidance (Garrity et al., 1996; Hing et al., 1999; Schmucker et al., 2000; Stevens and Jacobs 2002; Weng et al., 2011), myoblast fusion during muscle fiber formation (Kaipa et al., 2013), regulation of intercellular bridges in germline cells during gametogenesis (Stark et al., 2021), and negative regulation of insulin receptor signaling pathway (Wu et al., 2011; Willoughby et al., 2017). A dock transcript was first isolated and sequenced in Drosophila melanogaster in a screen for P-element insertions leading to R cell projection defects (Garrity et al., 1996). dock encodes a protein that contains three N-terminal SH3 domains and one C-terminal SH2 domain known to bind to specific motifs and serve as binding adaptors (Garrity et al., 1996). Its regulation of photoreceptor axon guidance in Drosophila occurs through its interaction with InR (Rao et al., 1998; Song et al., 2003; Rao 2005). The dock protein plays a role in negatively regulating the insulin signaling pathway by facilitating the dephosphorylation of InR through recruitment of the ER-localized form of protein tyrosine phosphatase PTP61F, a function that is also observed in its mammalian ortholog Nck (Wu et al., 2011; Buszard et al., 2013).

Synteny

dock occurs on chr2L in D. melanogaster and is flanked by upstream genes CG3662 and CG3862 and downstream genes drongo ( drongo ) and CG4291 . It has been determined that the putative ortholog of dock is found on scaffold KB465133.1 in D. eugracilis (GB2 assembly GCA_000236325.2 ) with LOC108110918 ( XP_017075680.1 , via tblastn search with an e-value of 6e-164 and percent identity of 82.47%), where it is surrounded upstream by LOC108110994 ( XP_017075791.1 ) and LOC108110993 ( XP_017075790.2 ) which correspond to CG3662 and CG3862 in D. melanogaster with e-values of 0.0, and percent identity of 89.04% and 93.39%, respectively, as determined by blastp ( Figure 1A, Altschul et al., 1990). The putative ortholog is flanked with downstream genes LOC108110973 ( XP_017075764.2 ) and LOC108110491 ( XP_017075058.1 ) which correspond to drongo and CG4291 in D. melanogaster with e-values of 0.0, and percent identity of 85.61% and 86.98%, respectively, as determined by blastp . This is likely the correct ortholog assignment for dock in D. eugracilis for three reasons: first, a tblastn search with D. melanogaster dock-PA sequence against the D. eugracilis genome generated a top hit at this location with an E-value of 6e-164 and a percent identity of 82.475%. Second, a blastp search with the peptide sequence from D. eugracilis ( XP_017075680.1 ) against the refseq_protein database in D. melanogaster generated a top hit of dock-PD with an e-value of 0.0 and percent identity of 87.43%. Third, the local synteny is highly conserved between the two genomic neighborhoods, with all the surrounding genes being orthologous to each other. The high similarity between the genomic neighborhood and gene identity is expected as D. eugracilis is closely related to D. melanogaster .

Protein Model

dock in D. eugracilis has encodes two unique protein isoforms; one encoded by mRNAs dock–RB , dock-RC , and dock-RD that all have identical CDSs, while dock-RA is unique ( Figure 1B ). All mRNA isoforms contain five CDSs. Relative to the ortholog in D. melanogaster , the RNA CDS number and protein isoform count are conserved. When comparing the protein alignment of dock-PB between D. eugracilis and D. melanogaster there is a high level of protein similarity and an 87.43% amino acid identity as determined by blastp ( Figure 1C ). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accessions BK064454 , BK064455 , BK064456 , and BK064457 . These data are also available in Extended Data files below, which are archived in CaltechData.

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., 2025).

Acknowledgments

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.

Funding Statement

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.

Extended Data

Description: A GFF, FASTA, and PEP of the model. Resource Type: Model. DOI: https://doi.org/10.22002/b9xm7-ren93

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Description: A GFF, FASTA, and PEP of the model. Resource Type: Model. DOI: https://doi.org/10.22002/b9xm7-ren93

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