Gene model for the ortholog of cnk in Drosophila erecta

Abstract

Gene model for the ortholog of connector enhancer of ksr (cnk) in the Dere_CAF1 Genome Assembly (GenBank Accession: GCA_000005135.1) of Drosophila erecta. 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:. cnk gene model comparison between Drosophila erecta and Drosophila melanogaster orthologs

(A) Synteny comparison of the genomic neighborhoods for cnk in Drosophila melanogaster and D. erecta. Thin underlying arrows indicate the DNA strand within which the target gene–cnk–is located in D. melanogaster (top) and D. erecta (bottom). The thin arrow pointing to the right indicates that cnk is on the positive (+) strand in D. erecta, and the thin arrow pointing to the left indicates that cnk is on the negative (−) strand in D. melanogaster. The wide gene arrows pointing in the same direction as cnk are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of cnk are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. erecta indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. erecta gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. erecta. (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of cnk in D. erecta are displayed in the User Supplied Track (black); 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. erecta), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster), RNA-Seq from Adult Males and Ovarian Follicle Cells (light blue and red respectively; alignment of Illumina RNA-Seq reads from D. erecta). (C) Dot Plot of cnk-PB in D. melanogaster (x-axis) vs. the orthologous peptide in D. erecta (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. (D) Conservation of 28 Drosophila species showing evolutionary conservation of cnk-PB as shown in D. melanogaster. The black regions in the ROAST Alignments for 28 Drosophila Species indicate conservation relative to D. melanogaster. This region shows high local sequence similarity to D. melanogaster in multiple species. The ROAST alignment for D. erecta is highlighted by the red box denoted I.