Using Comparative Genomics to Study DNA Sequences of the Muller F Element from Drosophila biarmipes

Abstract

The Genomics Education Partnership* (GEP) is a scientific and educational partnership using comparative genomics to characterize the Muller F element, a distinct chromosomal domain, from the genomes of several Drosophila species (see www.gep.wustl.edu). In Drosophila melanogaster, the F element corresponds to the fourth chromosome (or “dot” chromosome), which appears to be heterochromatic by many criteria, but has a relatively high gene density. Our goal is to study the evolution of these sequences to further our understanding of the function of heterochromatin. As part of an advanced genetics course at Albion College, we used several web-based tools to annotate a 50,000 base pair contiguous sequence from the genome of Drosophila biarmipes. The annotation process involved using the corresponding genomic region of the Drosophila melanogaster fourth chromosome as a reference sequence. Using BLAST we estimated the positions of each exon, then using a variety of evidence tracks from the UCSC genome browser, we precisely localized start codons, donor and acceptor splice sites, and stop codons for each isoform. Gene models were verified using the Gene Model Checker program and by generating final sequence alignments and dot plots using BLAST. Our analysis resulted in the annotation of five distinct genes in this contig. The genes ranged in complexity from 2-7 splice variants, with individual isoforms ranging in size from 4 to 12 exons each. Our analysis will be combined with data from other student members of the partnership to help answer questions about the organization and function of the Muller F element in several different species. *The Genomics Education Partnership is funded by HHMI (Professors grant #52007051 to SCR Elgin) and by Washington University in St. Louis (WUSTL).