The Paramecium genus provides a unique system for studying the effects of gene and genome duplication on organismal phenotype. It contains a number of distinct morphospecies together with numerous cryptic species, morphologically indistinguishable but biologically isolated from each other. The most famous such group is the P. aurelia species complex, consisting of ~15 distinct species, which is also remarkable for having undergone two whole-genome duplication (WGD) events not shared with other members of the Paramecium genus prior to its diversification. Paramecium is thus of great importance for our understanding of gene duplication and WGD events, their phenotypic effects, and the factors influencing the evolution of orthologous and paralogous genes and regulatory sequences. We address these issues by presenting a comprehensive comparative genomic analysis of members of the P. aurelia species complex together with several Paramecium species outside of the aurelia group.
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