Gene model for the ortholog of Ilp4 in Drosophila eugracilis

Abstract

Gene Model for Insulin-like peptide 4 (Ilp4) in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2). The characterization of this ortholog was carried out as part of a larger, ongoing dataset designed to explore the evolution of the insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, utilizing the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.

Keywords: Bioinformatics; Drosophila; Genomics; Genotype Data; New Finding.

Figure 1:. Ilp4 gene model comparison between Drosophila eugracilis and Drosophila melanogaster.

(A) Synteny comparison of the genomic neighborhoods for Ilp4 in Drosophila melanogaster and D. eugracilis. Thin underlying arrows indicate the DNA strand within which the target gene–Ilp4–is located in D. melanogaster (top) and D. eugracilis (bottom). The thin arrows pointing to the left indicate that Ilp4 is on the negative (−) strand in D. eugracilis and D. melanogaster. The wide gene arrows pointing in the same direction as Ilp4 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Ilp4 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. eugracilis indicate orthology to the corresponding gene in D. melanogaster, while grey gene arrows indicate a gene insertion in D. eugracilis. Gene symbols 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 GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Ilp4 in D. eugracilis are displayed in the User Supplied Track (black); coding exons 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. eugracilis), Spaln of D. melanogaster Proteins (light purple, alignment of Ref-Seq proteins from D. melanogaster), RNA-Seq from Adult Females and Mixed Embryos (red and dark purple, respectively; alignment of Illumina RNA-Seq reads from D. eugracilis), and Splice Junctions Predicted by regtools using D. eugracilis RNA-Seq (PRJNA63469). The splice junction which aligns with Ilp4 (JUNC00079282) has a read-depth of 657. (C) Dot Plot of Ilp4-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; coding-exon number is indicated along the top and right, and exons are also highlighted with alternating colors. The black diagonal lines indicate sequence similarity and are highlighted by the green box denoted I and the purple box denoted II. (D) Protein alignment between D. melanogaster Ilp4-PA and its putative ortholog in D. eugracilis. The alternating colored rectangles represent adjacent exons. The symbols in the match line denote the level of similarity between the aligned residues. An asterisk (*) indicates that the aligned residues are identical. A colon (:) indicates the aligned residues have highly similar chemical properties—roughly equivalent to scoring > 0.5 in the Gonnet PAM 250 matrix (Gonnet et al., 1992). A period (.) indicates that the aligned residues have weakly similar chemically properties—roughly equivalent to scoring > 0 and ≤ 0.5 in the Gonnet PAM 250 matrix. A space indicates a gap or mismatch when the aligned residues have a complete lack of similarity—roughly equivalent to scoring ≤ 0 in the Gonnet PAM 250 matrix. The green box denoted I and the purple boxes denoted II correspond to the boxes in figure 1C, respectively.