Gene model for the ortholog of Glyp in Drosophila pseudoobscura

Abstract

Gene model for the ortholog of Glycogen phosphorylase (Glyp) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly of D. pseudoobscura (GCA_000001765.2). 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:. Glyp gene model comparison between Drosophila pseudoobscura and Drosophila melanogaster orthologs

(A) Synteny comparison of the genomic neighborhoods for Glyp in Drosophila melanogaster and D. pseudoobscura. Thin underlying arrows indicate the DNA strand within which Glyp is located in D. melanogaster (top) and D. pseudoobscura (bottom). The thin arrow pointing to the right indicates that Glyp is on the positive (+) strand in D. melanogaster, and the thin arrow pointing to the left indicates that Glyp is on the negative (−) strand in D. pseudoobscura. The wide gene arrows pointing in the same direction as Glyp are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Glyp are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. pseudoobscura indicate orthology to the corresponding gene in D. melanogaster, while black gene arrows indicate non-orthology. Gene symbols given in the D. pseudoobscura gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. pseudoobscura. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Glyp in D. pseudoobscura 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. pseudoobscura), 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 and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. pseudoobscura), and Splice Junctions Predicted by regtools using D. pseudoobscura RNA-Seq (SRP006203). Splice junctions shown have a minimum read-depth of 1000 with >1000 supporting reads indicated in red. (C) Dot Plot of Glyp-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. pseudoobscura (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.