Genomic Analysis of the Allotetraploid Frog , Xenopus laevis

Genomic Analysis of the Allotetraploid Frog, Xenopus laevis by Adam M Session Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Daniel S. Rokhsar, Chair Duplication has long been recognized as an evolutionary source of novelty. The relaxation of purifying selection following duplication allows for normally deleterious mutations to persist long enough to give rise to novel phenotypes. Whole-genome duplications (WGDs) are a specific type of duplication, in which a species suddenly finds itself with two copies of all of its genomic loci. While the fate of most of the duplicated loci is to be lost, those that persist are thought to underlie the innovations seen in groups with a history of polyploidy, such as flowering plants, yeast, Paramecium, and vertebrates. These ancient events give us an idea of how WGDs can drive the radiation of large and diverse phyla, but do not give us any information on the genomic response immediately following polyploidy. This thesis provides insights into the origins of polyploidy and its effects on genome dynamics. There are two models for the mechanism of polyploidy: autopolyploidy and allopolyploidy. Autopolyploids are formed by doubling the somatic chromosomes in the zygote or early embryo. Allopolyploids are formed by the hybridization of two related, but genetically distinct, species, followed by chromosome doubling. If there are no extant diploid relatives, it can be difficult to distinguish between these two models. One feature of allopolyploids is the lack of recombination between their homeologous chromosomes. The end result is that any markers that were unique to each species while apart, such as transposable element subfamilies, will be asymmetrically distributed on the progenitor chromosomes in an organism that recently underwent a WGD. Xenopus laevis is an important vertebrate model in developmental and cell biology that has experienced a recent WGD (~40 million years ago [MYA], based on cDNA alignments (Hellsten, 2007). Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. Comparative analysis of these two frog genomes gives us an excellent opportunity to study genome dynamics following whole genome duplication. The discovery of asymmetrically distributed transposon subfamilies supports the model that cross-species hybridization through allotetraploidy is the mechanism underlying the polyploid Xenopus radiation. Thus, the subgenome sequence divergence of 40 MYA dates the divergence of the progenitor species, not the hybridization event. The asymmetric distribution of these elements between homeologous sequences allows us to assign chromosomes to progenitor species, named “A” and “B”, making X. laevis a unique system to study sub-genome-specific evolution. The wealth of transcriptome and epigenetic data available for Xenopus allows me to assay how these genomic changes affect gene expression as well as gene retention. The combination of these resources with genomic data gives me the resolution needed to date the hybridization both by studying the decay of unitary pseudogenes and by comparative analysis of the transposable elements discussed above. The sub-genome from progenitor species “A” has more assembled length, longer chromosomes, a higher rate of gene retention, and higher average expression in the adult frog. The B sub-genome has higher synonymous and nonsynonymous mutation rates. The chromosomes orthologous to X. tropicalis 9 and 10 are fused in both sub-genomes of X. laevis, forming homeologous chromosomes 15 and 18, and deviate from the A/B trends discussed above. The regions of these X. laevis chromosomes orthologous to X. tropicalis chromosome 10 have a lower density of diagnostic repeats, no sub-genome bias in gene retention, and have a higher silent substitution rate. This divergence from the rest of the genome is not shared by the