Annotation of Contig53 on Chromosome 3L of Drosophila takahashii

Abstract

DNA wraps around histones to form chromatin in the nucleus of eukaryotic cells. DNA densely packed histones, heterochromatin, is associated with silencing or transcription inactive genes. While, the loosely packed chromatin, euchromatin, is associated with actively transcribed genes. The F element, dot chromosome in Drosophila melanogaster is composed of mostly heterochromatin, yet has active transcribed genes. The goal of our research is to elucidate the regulatory motif within the dot chromosome by comparing the dot chromosome genes with gene located in the euchromatin, D element. In this study, Contig 53 in D element from Drosophila takahashii is characterized with 7 features. Through the creation of a gene model or outline of where exons and introns begin and end, instances of where regulatory motifs occurs can be observed. The Genome Browser allows for visualization of the predicted genes and isoforms. BLAST allows for the alignment of genes between the two species. FlyBase contains genetic and molecular data for Drosophila melanogaster. By annotating and comparing different contigs or gene segments of the two species and the divergence between two different species D. melanogaster and D. takahashii can be visualized as well as any silencing of genes that has occurred through evolution. Our research shows that although many of the jim isoforms vary slightly, data can be correlated with RNA seq, Gene scan predications, and TopHat predictions. Of 11 total isoforms of D. melanogaster, seven share almost 90% similarity to D. takahashii. This shows that through evolution, contig 53 of D. takahashii and D. melanogaster have only diverged marginally.Support or Funding InformationThis project was supported in part by grants from the Department of Education (Award #P031S150199), from Southern California Edison, and through Vanguard University’s SURP Program generously supported by the Office of the Provost and the Institute for Faculty Development.”Special thanks to the Genomics Education Partnership (GEP)