Resolution of Whole-Genome Duplications in Paramecium Species

Whole-genome duplications (WGD; polyploidization) can have significant and lasting effects on a species and its descendent lineages, and have played a role in the evolution of many lineages, including vertebrates.  New gene duplicates provide substrates for the evolution of novel genes and gene functions, and differential loss of duplicate genes in subpopulations may lead to reproductive isolation and rapid speciation.  The genomes of Paramecium aurelia species shows evidence of three past WGDs (Aury et al. 2006), and the most recent genome duplication shortly predates the rise of the P. aurelia species complex of 15 morphologically identical species. We are sequencing the genomes of all P. aureliaspecies and several out-group species, as well as generating RNA seq data, in order to follow the outcomes of WGD in each species.

Our initial genomes indicate a complicated story of differential gene lost in lineages, a surprisingly high rate of gene conversion between paralogs, and fundamental differences in mutation spectrum. With the completion of two out-group species’ genomes, P. caudatum and multimicronucleatum, we are developing a much better understanding of the genome structures that predated the P. aurelia WGD.