Gene model for the ortholog of Roc1a in Drosophila eugracilis

Abstract

Gene model for the ortholog of Regulator of cullins 1a ( Roc1a ) in the Drosophila eugracilis Apr. 2013 (BCM-HGSC/Deug_2.0, DeugGB2) Genome Assembly (GenBank Accession: GCA_000236325.2). 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. Roc1a gene model comparison between Drosophila eugracilis and Drosophila melanogaster orthologs

(A) Synteny comparison of the genomic neighborhoods for Roc1a in Drosophila melanogaster and D. eugracilis . Thin underlying arrows indicate the DNA strand within which the reference gene– Roc1a –is located in D. melanogaster (top) and D. eugracilis (bottom) genomes. The thin arrow pointing to the right indicates that Roc1a is on the positive (+) strand in D. melanogaster , and the thin arrow pointing to the left indicates that Roc1a is on the negative (-) strand in D. eugracilis . The wide gene arrows pointing in the same direction as Roc1a are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of Roc1a 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 black gene arrows indicate non-orthology. 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 Roc1a in D. eugracilis 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. eugracilis ), 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. eugracilis ), and Splice Junctions Predicted by regtools using D. eugracilis RNA-Seq (PRJNA63469). Splice junctions shown have a minimum read-depth of 10 with >1000 supporting reads shown in red. (C) Dot Plot of Roc1a-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; CDS number is indicated along the top and right, and CDSs are also highlighted with alternating colors . (D) Model of Roc1a-PA compared to Roc1a-PC in Apollo. A screenshot of the Apollo instance housing the proposed gene model of Roc1a-PA (identical to that of Roc1a-PD) and the likely absent Roc1a-PC model, containing in frame stop codons. The proposed models are shown at the top in the yellow region, while evidence tracks are found below in the white region. CDS reading frames are indicated in blue, green, and red, and implausible CDS sequence warnings (in this case due to the in-frame stop codons) are indicated in white. Evidence tracks from top to bottom include Transcripts and Coding Regions Predicted by TransDecoder and RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. eugracilis ; PRJNA63469).