Mitotic recombination and rapid genome evolution in the invasive forest pathogen Phytophthora ramorumm

Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. NA1 is responsible for sudden oak death in the USA, NA1, NA2 and EU1 are responsible for ramorum blight in the USA and Canada and EU1 and EU2 are responsible for sudden larch death and blight in Europe. We sequenced 107 genomes to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in putative pathogenicity genes was fixed in NA1. An independent ROH affected the same scaffold in EU1 suggesting an MR hotspot and selection target. EU1 individuals with and without the ROH ...