Genome Annotation of Drosophila Biarmipes Dot Chromosome Contig 38

The small “dot” chromosome (Muller F element) of D. melanogaster exhibits unique properties, making it the focus of a comparative genomics study organized by the Genomics Education Partnership (GEP; http://gep.wustl.edu) at Washington University in St. Louis.  This chromosome exhibits many heterochromatic features, including a high density of repeats, lack of meiotic recombination, late replication, and association with heterochromatic proteins.  Nonetheless, it contains ~80 genes.  A comparative genomic analysis of Muller F elements of Drosophila species should provide insights into the nature of heterochromatin formation and evolution.  GEP students have completed sequence improvement and analysis of the D. virilis, D. erecta, D. mojavensis and D. grimshawi dot chromosomes, to look at the patterns over 40 million years of evolution. We are now working on the F element chromosome and a euchromatic reference region of D. biarmipes, a species closely related to D. melanogaster, which should facilitate identifying dot chromosome regulatory motifs. The goal of this project was to annotate the genes of D. biarmipes dot chromosome contig 38. Basic Local Alignment Search Tool (BLAST) was used along with Gene Record Finder to compare the protein sequence of D. melanogaster exons to the D. biarmipes contig in order to locate the placement of the homologous exons in the latter species. Gene prediction programs were used to examine regions of the genome not immediately shown to contain genes. Additional tools such as RNAseq data and multiple BLAST analyses were used to confirm the gene models. The information was entered into Gene Model Checker to confirm the alignments, and a comprehensive map of the contig was compiled. Two genes were found on contig38, Slip1 and gw, with 3 and 6 isoforms, respectively. Slip1 isoforms all had unique coding regions, unlike the isoforms of gw, which shared identical coding regions in its 6 isoforms.  Results indicate no significant changes in splice sites, for either the Slip1 nor the gw gene in D. biarmipes compared to D. melanogaster. Overall, both genes showed a high degree of homology with their D. melanogaster orthologs.  We also present preliminary annotation of transcriptional start sites (TSS) in D. biarmipes, an analysis that will facilitate a search for regulatory elements based on conservation among species.