Date of Award
College of Arts & Sciences
Bachelor of Arts
At 4.2 Mb overall, the Drosophila melanogaster Muller F element (dot chromosome) is an unusual autosome; it is broadly heterochromatic, but the distal 1.3 Mb has a gene density and expression pattern similar to other autosomes. More intriguing is the large expansion of the D. ananassae F element (~20 Mb). Elucidating the factors that contribute to this expansion could improve our understanding of how heterochromatic domains are maintained and amplified.
Previous analyses show that the lateral gene transfer (LGT) of Wolbachia (the most widespread intracellular bacteria in the Rickettsiales order) into the D. ananassae genome is an important contributor to the expansion of the F element. Because many genes in the Wolbachia endosymbiont of D. ananassae (wAna) have not been characterized, I used multiple bioinformatics programs to compare the genome assemblies of wAna with wMel and wRi to improve the wAna gene annotations. Collectively, I assigned classifications for ~30% of the wAna genes with unknown functions (i.e. predicted hypothetical proteins). Consistent with previous reports, I also found a high density of Insertion Sequence (IS) transposon remnants within the three Wolbachia genomes, particularly in wAna. These IS sequences might facilitate the LGT of wAna and contribute to the expansion of the D. ananassae F element.
Analysis of three improved D. ananassae F element scaffolds (~1.4 Mb) showed that 65 out of 415 unclassified repeats identified by RepeatMasker have similarity to wAna, suggesting that many of these Unknown repeats might be derived from Wolbachia. We also compared the distribution of wAna genomic scaffolds within introns and intergenic regions as well as identified genomic regions and proteins in wAna that are overrepresented in the D. ananassae F element.
Collectively, this study will increase our knowledge of the factors that affect chromatin packaging and the evolutionary impact of endosymbionts on host genomes.
Chen, Elizabeth J., "Investigating the Role of Wolbachia Endosymbionts in the Expansion of the F Element in Drosophila ananassae" (2015). Undergraduate Theses—Unrestricted. 27.