Gene model for the ortholog of Pdk1 in Drosophila grimshawi

Abstract

Gene model for the ortholog of Phosphoinositide-dependent kinase 1 ( Pdk1 ) in the May 2011 (Agencourt dgri_caf1/DgriCAF1) Genome Assembly (GenBank Accession: GCA_000005155.1 ) of Drosophila grimshawi . 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 Pdk1 in Drosophila grimshawi

(A) Synteny of genomic neighborhood of Pdk1 in D. melanogaster and D. grimshawi . Gene arrows pointing in the same direction as the reference gene in both D. grimshawi and D. melanogaster are on the same strand as the reference gene; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrow pointing to the right indicates that Pdk1 is on the + strand in D. melanogaster ; and the thin arrow pointing to the left indicates that Pdk1 is on the – strand in D. grimshawi . White arrows in D. grimshawi indicate the locus ID and the orthology to the corresponding gene in D. melanogaster and black arrows indicate a non-orthologous gene. The gene names given in the D. grimshawi gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. grimshawi . The gene with LOC6556806 was present in D. grimshawi but did not have an ortholog in D. melanogaster. (B) Gene Model in UCSC Track Hub (Raney et al., 2014) : the gene model in D. grimshawi (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. grimshawi ), RNA-Seq from adult females (red) and adult males (blue) (alignment of Illumina RNAseq reads from D. grimshawi ), and Transcripts (green) including coding regions predicted by TransDecoder and Splice Junctions Predicted by regtools using D. grimshawi RNA-Seq ( SRP073087 ). Splice junctions shown have a minimum read-depth of 55 with 50-99 and 100-499 supporting reads in green and pink, respectively. The custom gene model (User Supplied Track) is indicated in black with CDS depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Pdk1-PD in D. melanogaster ( x -axis) vs. the orthologous peptide in D. grimshawi ( 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. Box A highlights a tandem repeat present in CDS 3, and box B shows a region with low sequence similarity and an indel in CDS 4. (D) Partial protein alignment of Pdk1-PD in D. melanogaster vs. the orthologous peptide in D. grimshawi . 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. The boxed regions in figure C contain idiosyncrasies that have been further highlighted in the protein sequence alignment in figure D, with box A showing a tandem repeat and box B showing a region containing an indel and low sequence similarity.