Gene model for the ortholog of foxo in Drosophila sechellia

Abstract

Gene model for the ortholog of forkhead box, sub-group O (foxo) in the May 2011 (Broad dsec_caf1/DsecCAF1) Genome Assembly (GenBank Accession: GCA_000005215.1) of Drosophila sechellia. 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.

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

Figure 1:. foxo gene model comparison between Drosophila sechellia and Drosophila melanogaster orthologs

(A) Synteny comparison of the genomic neighborhoods for foxo in Drosophila melanogaster and D. sechellia. Thin arrows indicate the DNA strand within which the target gene– foxo –is located in D. melanogaster (top) and D. sechellia (bottom). The thin arrow pointing to the left indicates that foxo is on the negative (−) strand in D. sechellia, and the thin arrow pointing to the right indicates that foxo is on the positive (+) strand in D. melanogaster. The wide gene arrows pointing in the same direction as foxo are on the same strand relative to the thin arrows, while wide gene arrows pointing in the opposite direction of foxo are on the opposite strand relative to the thin arrows. White gene arrows in D. sechellia indicate orthology to the corresponding gene in D. melanogaster. Gene symbols given in the D. sechellia gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. sechellia (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of foxo in D. sechellia 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. sechellia), 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. sechellia), Splice Junctions Predicted by regtools using D. sechellia RNA-Seq (McManus et al., 2014, Ma et al., 2018; PRJNA205470, PRJNA414017). The splice junctions pertaining to the foxo ortholog, have a minimum read-depth of 55 with 50–99 and 100–499 supporting reads in green and pink respectively. (C) Dot Plot of foxo-PG in D. melanogaster (x-axis) vs. the orthologous peptide in D. sechellia (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. Line breaks in the dot plot indicate mismatching amino acids at the specified location between species. The box in figure C (1C-i) shows a region of LINE repeats in the protein sequence. (D) Model in UCSC Track Hub demonstrating the lack of data to support the existence of foxo-PH isoform in D. sechellia (Raney et al. ,2014).