Repeat mediated gene duplication in the Drosophila pseudoobscura genome

Genetic mutations can occur on a wide variety of scales, including those that change single nucleotides, those that add or remove content to/from a genome, and those that change the organization of a genome. Gene duplications are a specific class of mutations that add content to a genome, and they can arise via a wide variety of mechanisms. I examined the mechanisms responsible for recently duplicated genes in the D. pseudoobscura genome, and I observed both retroposed and DNA duplications. Many duplicated genes lack signatures of either retroposition or DNA-based mechanisms, but other features of these ambiguously duplicated genes suggest that most were generated via retroposition. Furthermore, close examination of sequences flanking DNA duplications and those found at the breakpoints of chromosomal inversions suggests a connection between these two events. In Drosophila, duplicated genes near inversion breakpoints can arise via unequal genetic exchange during the non-allelic crossing over event giving rise to the inversion. I observed one duplicated gene in the D. pseudoobscura genome that appears to have been generated by this mechanism. Additionally, many DNA duplications in the D. pseudoobscura genome are flanked by a repetitive sequence also found at the breakpoints of chromosomal inversions. This suggests that the molecular mechanisms responsible for chromosomal rearrangements and some duplicated genes have overlapping processes.