Gene model for the ortholog of Ilp3 in Drosophila ananassae

Abstract

Gene model for the ortholog of Insulin-like peptide 3 ( Ilp3 ) in the May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of Drosophila ananassae . 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 Ilp3 in Drosophila ananassae :

(A) Synteny comparison of the genomic neighborhoods for Ilp3 in Drosophila melanogaster and D. ananassae . Thin underlying arrows indicate the DNA strand within which the reference gene– Ilp3 –is located in D. melanogaster (top) and D. ananassae (bottom). The thin arrow pointing to the right indicates that Ilp3 is on the positive (+) strand in D. ananassae , and the thin arrow pointing to the left indicates that Ilp3 is on the negative (-) strand in D. melanogaster . The wide gene arrows pointing in the same direction as Ilp3 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Ilp3 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. ananassae indicate orthology to the corresponding gene in D. melanogaster . Gene symbols given in the D. ananassae gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. ananassae . (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of Ilp3 in D. ananassae 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. ananassae ), 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. ananassae ), and Splice Junctions Predicted by regtools using D. ananassae RNA-Seq ( SRP006203 , SRP007906 , PRJNA257286 , PRJNA388952 ). Splice junctions shown have a minimum read-depth of 10 with 10-49, 50-99, 100-499, 500-999, and >1000 supporting reads in blue, green, pink, brown, and red, respectively. (C) Dot Plot of Ilp3-PA in D. melanogaster ( x -axis) vs. the orthologous peptide in D. ananassae ( y -axis). Amino acid number is indicated along the left and bottom; coding-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. The line breaks shown are small and determined to be insignificant in the determination of the putative ortholog of Ilp3 in D. ananassae . (D) Protein alignment between D. melanogaster Ilp3-PA and its putative ortholog in D. ananassae . The alternating colored rectangles represent adjacent CDSs. 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.