The Drosophila Dot Chromosomes
Our current projects center around the dot chromosome (F element) of Drosophila. This small chromosome is entirely heterochromatic by many measures, including dense staining, late replication, no meiotic combination, and association with high levels of HP1 and H3K9me3. However, the 1.3 Mb distal portion contain ~80 genes, exhibiting a gene density typical of the euchromatic domains. Our comparative analysis using several Drosophila species is allowing us to examine the characteristics of the genes and overall organization of this unique domain, as well as revealing how such a domain changes over evolutionary time. Recently we completed sequence improvement and annotation of the F element, and a comparison euchromatic domain from the D element, from three species covering 40 million years of evolutions, D. grimshawi, D. mojavensis, and D. erecta for comparison with D. melanogaster (Leung et al. 2015). Our current project involves sequence improvement and annotation of a group of species that diverged from D. melanogaster about 10 million years ago. We want to use phylogenetic footprinting to see if we can identify motifs specific to the F element, and this evolutionary distance represents the "sweet spot" for identifying such elements based on conservation. A second on-going project is investigation of a small number of Drosophila species that have a greatly expanded F element, creating a domain that is 80% repeats — while maintaining gene function! More details …
Members of the GEP are currently developing opportunities to collaborate with scientists working on gut bacteria and on the Puerto Rican parrot. Our recently funded project with Galaxy will make it easier to create good genome browser pages for annotation of any sequenced genome. In the long run, we anticipate developing a website that can connect our members to annotation projects in a wide range of eukaryotes.