Genome-wide analyses resolve three clonal lineages and lineage-specific ploidy in Phytophthora cinnamomi

Phytophthora cinnamomi is a globally invasive oomycete that causes root rot and dieback in thousands of plant species threatening both avocado production and native vegetation in South Africa. Previous simple sequence repeat analyses revealed a largely clonal population structure comprising three lineages and suggested widespread triploidy. To obtain a genome-wide view of population structure, ploidy and recombination, we analysed whole-genome sequencing data for 49 South African isolates previously characterised with SSRs and three additional isolates with known mating types from Australia, together with publicly available genomic data from 33 additional isolates from Australia (three isolates), Indonesia (one isolate), New Zealand (27 isolates), and the USA (two isolates). Population genomic analyses consistently resolved the isolates into three distinct lineages, broadly congruent with those previously identified using SSR data and in a recent global phylogeographic study of P. cinnamomi . Isolates from avocado orchards occurred predominantly in two of the lineages, whereas a third lineage largely comprised isolates from natural vegetation. Ploidy profiling using short-read sequencing data indicated that most isolates in the first two lineages were triploid, while all nine isolates in the third lineage, most of which originated from natural vegetation, were diploid. The absence of admixture among lineages and limited signatures of recent recombination supported a predominantly clonal mode of reproduction in this species. Together, these results support the presence of three well-differentiated lineages in the P. cinnamomi isolates analysed in this study. The occurrence of two predominantly triploid lineages and their apparent association with avocado-derived isolates is an intriguing pattern that warrants further investigation into the potential roles of polyploidy and genome plasticity in the evolution and ecological distribution of these lineages.