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

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
Affiliations

Gene model for the ortholog of Myc in Drosophila eugracilis

Megan E Lawson et al. MicroPubl Biol. .

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.

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Conflict of interest statement

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

Figures

Figure 1.
Figure 1.
(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.
See this image and copyright information in PMC

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