Insights Into The Transmission Of Helitrons And Their Impact On The Genome Architecture Of Myotis Lucifugus, The Little Brown Bat

Abstract

Probably the most dynamic proportion of multicellular eukaryotic genomes is composed of teeming populations of parasitic mobile DNA, called transposable elements (TEs). Helitrons are rolling circle TEs that have a limited distribution among mammals, having been identified only in the genome of the little brown bat, Myotis lucifugus, and a few closely related species. One family of Helitrons, called Helibat, was estimated to make up as much as 3% of the M. lucifugus genome. In addition, Helibat was shown to have captured and amplified the promoter and 5' UTR of a highly conserved single copy gene to >1000 copies. Together these observations led to the hypothesis that Helitrons have profoundly shaped the evolutionary trajectory of M. lucifugus and formed the impetus for this work. We sought to address questions concerning the distribution of Helitrons among bats, the role of horizontal transfer (HT) in explaining their patchy distribution and their impact in the M. lucifugus genome. To this end, we employed a combination of in silico, PCR and DNA hybridization based approaches. We provide for the first time evidence for HT of Helitrons (Appendix A). Our analyses revealed a family of Helitrons found in M. lucifugus as well as an array of distantly related animals, including reptiles, fish, invertebrates, and insect viruses. Most of the HT Helitrons were identified in insects and led us to speculate that the abundance of insects eaten on a daily basis by insectivorous bats might in part influence their propensity for HT. To investigate this hypothesis and to determine the presence of protein coding Helitrons in other bat genomes, we examined 83 bat genomes representing ten families with diverse eating habits. These analyses revealed that protein coding Helitrons could only be identified in vesper bats and were not detected in a broad range of phyllostomid bats with diverse diets or species representative of any of the other families of bats (Chapter 2). These results suggest that feeding habits alone are not sufficient to explain HT. Finally, we executed a comprehesive analysis of Helitrons in the M. lucifugus genome (7X coverage) (Chapter 3). This analysis revealed 37 families and 59 subfamilies that contribute to a total of 11.5% of the genome. This is the highest percentage of Helitrons ever described in any genome. Through this analysis we show that Helitrons have captured promoters, 5' UTRs, 3' UTRs, coding exons and introns of several genes that are well conserved in mammals. These Helitrons were further amplified to thousands of copies in some cases. In addition, Helitrons have mediated the amplification of several retrogenes. Helitrons through HT and amplification have profoundly impacted the genomic architecture of vesper bats and it is tempting to speculate that they tremendously influenced their evolutionary trajectory.