Subgenome evolution and sex chromosome conservation through multiple allotetraploidization events in the African clawed frogs (Xenopus)

Abstract

Allotetraploid genomes possess two subgenomes with potentially distinct characteristics such as gene function, expression, recombination, and transposable element mobility. To test if population structure and gene flow also differ between subgenomes, in my PhD thesis second chapter, I analyzed genetic variation in the allotetraploid African clawed frog (Xenopus laevis) across its native range in southern Africa. Analysing Reduced Representation genomic data from 91 samples across 12 locations, we found no strong evidence for difference in population structure or differential gene flow between subgenomes. Comparing nuclear data to mitochondrial sanger sequences from 455 samples across 183 locations, our findings refine the geographic distribution of diversity in this species. We observed that population structure in both genomes generally aligns with seasonal rainfall patterns and southern African topography. Genome duplication can fuel evolution by creating genetic redundancy, potentially leading to novel gene functions or reduced pleiotropic constraints. African clawed frogs (Xenopus) are notable for their high rate of sex chromosome turnover, which has been hypothesized to be linked to the genus's multiple polyploidization events. I tested this in my third chapter analysing genomes of the Silurana group, mapping sex-linked regions in three allotetraploid species and examining variation in the diploid X. tropicalis. This revealed at least two independent allotetraploidization events, geographic genetic structure and sex-linked variation in X. tropicalis. However, the conservation of sex-linked regions between diploids and allotetraploids, and evidence for homologous sex chromosomes in X. calcaratus, and X. tropicalis along with insights into the divergence of a Liberian X. tropicalis lineage and admixture in a Nigerian contact zone, suggest that polyploidization is not a major catalyst for sex chromosome turnover in Xenopus.