Natural Variation And Divergence Of Repetitive Dna In Drosophila

Abstract

Most eukaryotic genomes harbor substantial amounts of transposable elements and satellite DNA, collectively known as repetitive sequences. They are characterized as genomic parasites as they increase copy number often at the expanse of host fitness. Because activities of these elements can cause genomic instability, they are usually highly regulated and maintained in the repressive chromatin environment known as heterochromatin. Yet, there are many examples where repetitive DNA adopts crucial cellular functions, including recruiting centromeric proteins and extending telomeres. Additionally, they are often evolving at high rates such that closely related species have vastly different types and abundances of repetitive sequences. However, the evolutionary dynamics of repetitive sequences and mechanisms driving their rapid turnover remain elusive. Here, I present several methods and studies that shed light on to the evolution of repetitive sequences. In the first study, I present k-Seek, a computational method to identify and quantify simple sequence repeats from whole genome sequences. Using this method, we characterized variation in satellite DNA in Drosophila melanogaster natural populations. In the second study, I applied k-Seek on nine Drosophila species, to determine the divergence pattern of satellite DNA. I find that the rapid turnover of satllites is not universal but specific to only some fly lineages. In the third study, I investigated one mechanism, known as meiotic drive, by which repeats can evolve rapidly. I present a novel method to identify meiotic drivers utilizing pooled sequencing. This method was used to test whether different abundances of the telomeric retrotransposon HeT-A, and by extension telomere length, can bias chromosome transmission. In the last study, I examined one striking consequence of the rapid divergence of repetitive DNA - hybrid incompatibility. Using RNA-Seq, I examined, transcriptome-wide, the mis-regulation in hybrids associated with the lethality caused by the Hybrid Male Rescue gene which regulates the expression of repetitive sequences in D. melanogaster and D. simulans.