Gene model for the ortholog of Ilp4 in Drosophila grimshawi

Abstract

Gene Model for the Insulin-like peptide 4 (Ilp4) ortholog in the D. grimshawi (dgriCAF1) assembly (GeneBank Accession: GCA_000005155.1) of Drosophila grimshawi. The characterization of this ortholog was conducted as part of a broader, developing dataset aimed at investigating the evolution of the Insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, using the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.

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

Figure 1:. Ilp4 gene model comparison between Drosophila grimshawi and Drosophila melanogaster.

(A) Local synteny of genomic neighborhood of Ilp4 in D. melanogaster and D. grimshawi. Gene arrows pointing in the same direction as the target gene (Ilp4) in both D. grimshawi and D. melanogaster are on the same strand as the target gene; gene arrows pointing in the opposite direction are on the opposite strand. The thin underlying arrows pointing to the right indicate that Ilp4 is on the + strand; arrows pointing to the left indicate that Ilp4 is on the – strand. White arrows in D. grimshawi indicate the locus ID and the orthology to the corresponding gene in D. melanogaster. Gray arrows indicate paralogs of a duplication of downstream gene Ilp2 that is not present in D. melanogaster. The gene names given in the D. gimshawi gene arrows indicate the orthologous gene in D. melanogaster, while the locus identifiers are specific to D. grimshawi. (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 males (blue) and adult females (red), 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). The custom gene model (User Supplied Track) is indicated in black with exon depicted with wide boxes, intron with narrow lines (arrows indicate direction of transcription). (C) Dot Plot of Ilp4-PA in D. melanogaster (x-axis) vs. the orthologous peptide in D. grimshawi (y-axis). Amino acid number is indicated along the left and bottom; exon number is indicated along the top and right, and exons are also highlighted with alternating colors. There are large gaps in the dot plot which indicates dissimilarity in the amino acid sequence between Ilp4-PA in D. melanogaster and D. grimshawi.