Final Annotation Report

Drosophila elegans F Element Project: contig11 Bio 434W Daniel Cui Zhou 04/27/15 Abstract: Contig11, part of the dot (fourth) chromosome in Drosophila elegans, was annotated using a variety of bioinformatics tools, including the Basic Local Alignment Search Tool (BLAST), the UCSC Genome Browser, and gene predictors such as GENSCAN and N-SCAN, as well as RNA-Seq data and TopHat junctions. The Drosophila melanogaster genome was used as a reference for gene orthology. Four genes were annotated in contig11, ATPsynbeta, CaMKII, Zyx, and Rfabg. All genes except Rfabg had one missing isoform compared to their respective D. melanogaster orthologs. The missing isoforms in each case are most likely due to the evolution of a new isoform in D. melanogaster, since only very closely related fly species, such as D. yakuba and D. erecta share the new isoform. Zyx has an additional exon that could be unique to D. elegans. The transcription start site (TSS) of ATPsynbeta was found to be part of a peaked promoter. Due to the lack of evidence aside from homology, a search region was proposed in addition to the exact coordinates of the TSS.19.67% of contig11 is composed of repetitious sequences, with only three repeats spanning more than 500 bases (2 helitrons and 1 unknown repeat). All four genes are syntenic with respect to D. melanogaster. Additionally, D. melanogaster contains genes CG11076 and CG11077 and the non-coding RNA CR44031, but these all translocated together to a different part of the D. elegans genome.