Comparative Genomics of Phytophthora rubi and P. fragariae

Contrasting the genomes of sister taxa with narrow but different host ranges provides an ideal system for studying host range adaptation. We used the genomes of two sister oomycete plant pathogens to study genomic signatures of host adaptation: Phytophthora rubi, the main cause of root rot in red raspberry, and P. fragariae, which causes red root steele in strawberries. Prior to 2007, P. rubi was considered a taxonomic variety of the species P. fragariae. P. rubi has since been described as a new species. High host specificity has been reported for both species and no successful cross-infection of hosts has been reported, providing phenotypic support that underlying genetic mechanisms may have driven this host differentiation. We sequenced the genomes of these taxa using next-generation sequencing techniques to identify polymorphisms, nucleotide diversity and to infer selection. We were particularly interested in studying presence/absence polymorphism and mutations in effector proteins in the RxLR gene family. These genes, associated with the host-pathogen interaction, have been determined to be important in the divergence among other Phytophthora taxa and may play a role in host differentiation among the sister species P. rubi and P. fragariae.