Genomic evolution of polyploid yeast species

Abstract

In Chapter 2 of this thesis I study how the genome structure and content of yeast has evolved since a Whole Genome Duplication (WGD) occurred in the lineage approximately 100 million years ago. By using genome data from several extant species whose lineages arose both before and after the WGD, I parsimoniously reconstructed the genome order and content for the ancestor that existed immediately prior to the WGD. This ancestor contained at least 4703 loci, and there are 66 reciprocal translocations, 73 inversions, 5 Robertsonian translocations, 9 single-gene transpositions and 2 multigene transpositions found between the genome duplicated ancestor and the extant S. cerevisiae genome. Some of these rearrangements are phylogenetically informative because they are shared by one or more species to the exclusion of others. The phylogeny inferred by these shared rearrangements differs from most sequence-based phylogenies. There have been 153 genes gained in S. cerevisiae since the ancestor, and there are 144 loci in the ancestor that have been deleted in double copy in S. cerevisiae. Breakpoints created by rearrangements and the locations of gene gains are enriched for tRNA genes in S. cerevisiae. There is evidence of breakpoint reuse in rearrangements, and there is an average use of 1.22 rearrangements per breakpoint.