Two Phytophthora cinnamomi clonal lineages affecting avocado orchards in California exhibit phenotypic variability with a putative introduction from Mexico

Phytophthora cinnamomi is a devastating hemibiotrophic oomycete plant pathogen with a large host range and responsible for the destruction of natural ecosystems and economically important crops worldwide including avocado. Several P. cinnamomi population studies have been conducted within the past decade and all report the presence of clonal populations with one reporting variation in ploidy, however none of these studies employed a whole-genome resequencing approach. In this study, we performed a whole-genome population genomic study to elucidate the population structure of P. cinnamomi affecting avocado growing regions of California and Mexico. Results from this study will aid future P. cinnamomi population genomic studies and in the development of molecular diagnostic markers and P. cinnamomi resistant plants.