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. 2024 Aug 3;2024:10.17912/micropub.biology.000912. doi: 10.17912/micropub.biology.000912

Gene model for the ortholog of Myc in Drosophila eugracilis

Megan E Lawson 1, Alexa Hoffman 2, Isabel G Wellik 3, Jeffrey S Thompson 3, Joyce Stamm 2, Chinmay P Rele 1,§
Reviewed by: Sebastian Sorge
PMCID: PMC11330573  PMID: 39157808

Abstract

Gene model for the ortholog of Myc ( Myc ) 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.

Figure 1.

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(A) Synteny of genomic neighborhood of Myc 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 Myc and the downstream genes are on the + strand; the arrow pointing to the left indicates that the upstream genes are on the – strand in D. eugracilis . White arrows in D. eugracilis indicate the locus ID and the orthology to the corresponding gene in D. melanogaster, and gray arrows indicate that the orthologous genes upstream of Myc in D. melanogaster are found on a different scaffold in D. eugracilis than Myc . The brackets beneath the local synteny diagram for D. eugracilis show which scaffold each gene is found on. 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 RefSeq proteins from D. melanogaster ), BLAT alignments of NCBI RefSeq Genes (blue, alignment of RefSeq genes for D. eugracilis ), RNA-seq from female (red), male (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 (Chen et al. , 2014; PRJNA63469 ). Note that there is no measured expression of the first CDS of Myc (Flybase ID: 1_12880_0) in females (Flybase IDs from FB2022_03; Larkin et al., 2021). Splice junctions shown have a minimum read-depth of 702 with 500-999 and >1000 supporting reads in brown and red respectively. The custom gene model (User Supplied Track) is indicated in black with CDSs depicted by boxes and introns by narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Myc-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; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors. The gaps in the dot plot indicate regions with low sequence similarity. The region within the black box (box a) contains a tandem repeat in CDS 2 that is conserved across both D. melanogaster and D. eugracilis . The green box (box b) highlights low sequence similarity in CDS one (D) Idiosyncrasies in the protein alignment. CDS one, which is boxed in green (box b), has many segments with low amino acid sequence similarity between D. melanogaster and D. eugracilis . The black box (box a) indicates a tandem repeat in the second CDS.

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) .

“Myc acts downstream of the insulin signaling pathway, with Myc protein accumulating in response to insulin through transcriptional and post-transcriptional mechanisms (Parisi et al., 2011) , resulting in the activation of genes involved in anabolic processes that promote cell growth (Terakawa et al., 2022) . Myc encodes a basic helix-loop-helix transcription factor in Drosophila melanogaster that is homologous to vertebrate Myc proto-oncogenes (Gallant et al., 1996) . In Drosophila melanogaster , Myc transcriptionally regulates a wide range of genes, including those that influence cell growth and metabolism (Teleman et al., 2008; Gallant 2013) .” (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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The model presented here is the ortholog of Myc in the Apr. 2013 (BCM-HGSC/Deug_2.0) assembly of D. eugracilis ( GCA_000236325.2 ) and corresponds to the Gnomon Peptide ID ( XP_017065790.1 ) predicted model in D. eugracilis ( LOC108104317 ). This gene model is based on RNA-seq data from D. eugracilis (Chen et al., 2014; PRJNA63469 ) and the Myc (Drosophila 12 Genomes Consortium et al . , 2007; GCA_000001215.4 ) in D. melanogaster from FB2023_03 ( GCA_000001215.4 ; Larkin et al., 2021; Gramates et al., 2022).

Gene and species details can be found in the description above.

Synteny

Myc occurs on chromosome X in D. melanogaster and is flanked by ng4 and dnc upstream and CG12535 and CG14269 downstream . The upstream dnc gene in D. melanogaster nests Pig1, Sgs4, and CG10793 . We determined that the putative ortholog of Myc is found on the AFPQ02005162.1 scaffold in D. eugracilis (GB2 assembly GCA_000236325.2 ) with LOC108104317 ( XP_017065790.1 ) (via tblastn search with an e-value of 0.0 and percent identity of 68.18%). It is flanked downstream by LOC108104312 ( XP_017065785.1 ) and LOC108104315 ( XP_017065789.1 ), which correspond to CG12535 and CG14269 in D. melanogaster with e-values of 7e-72 and 6e-110 respectively, and percent identities of 55.83% and 79.47% respectively, as determined by blastp ( Figure 1A, Altschul et al ., 1990). Myc is the first gene on the AFPQ02005162.1 scaffold in D. eugracilis , so there are no upstream genes to analyze for local synteny. However, blastp results indicated that the orthologs of genes upstream of Myc in D. melanogaster are located on scaffold KB464875.1 in D. eugracilis with LOC108118138 ( XP_017086187.1 ) , LOC108118129 ( XP_041674349.1 ) , LOC108118132 ( XP_017086181.1 ) , and LOC108118131 ( XP_017086180.1 ), which correspond to ng4, dnc, Pig1, and CG10793 with e-values of 9e-22, 0.0, 2e-77, and 0.0, respectively, and percent identities of 82.76%, 95.42%, 58.33%, and 87.81% respectively, as determined by blastp ( Figure 1A, Altschul et al ., 1990). Local synteny was conserved within this part of the neighborhood in D. eugracilis as well, with the exception of Sgs4 , for which an ortholog in D. eugracilis could not be located. We believe this is the correct ortholog assignment for Myc in D. eugracilis because all of the BLAST hits had very low e-values and were the best BLAST result by a wide margin, and because local synteny is well-conserved throughout the genomic neighborhood.

Protein Model

Myc in D. eugracilis has one unique protein coding isoform encoded by mRNAs Myc-RA and Myc-RB, which differ in their UTRs ( Figure 1B ). Myc-PA/Myc-PB contain two protein coding CDSs. This is the same relative to the ortholog in D. melanogaster. The sequence of Myc in D. eugracilis has 67.0% identity with Myc in D. melanogaster as determined by blastp ( Figure 1C ). This is more divergence between the sequence than one would expect, considering how closely related D. melanogaster and D. eugracilis are. The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accessions BK063012 and BK063013 . These data are also available in Extended Data files below, which are archived in CaltechData.

Special characteristics of the protein model

Tandem repeat in CDS two

There is a tandem repeat present in CDS two in Myc , which is shown in figures C and D in black box a. Specifically, the repeat is made up of nine uninterrupted Serine amino acids present in the protein sequence.

Low sequence similarity in CDS one

There are many regions in CDS one of Myc that have very low conservation of their amino acid sequences between the two species. This is pictured in the green boxes (box b) in figures C and D.

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. eugracilis ( GCA_000236325.2 ) ) 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. 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 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.

Extended Data

Description: GFF, FASTA, and PEP of the model. Resource Type: Model. DOI: 10.22002/wtccf-p2596

Description: response to editorial pre-review. Resource Type: Text. DOI: 10.22002/c7079-pkh57

Acknowledgments

Acknowledgments

We would like to thank Wilson Leung for developing and maintaining the technological infrastructure that was used to create this gene model, Madeline L. Gruys and Logan Cohen for retrofitting this 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.

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.

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