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Analysis of global populations of Phytophthora cinnamomi suggests presence of two dominant clonal lineages and evidence of sex in Southeast Asia

Nik Grunwald: USDA-ARS, Horticultural Crops Research Unit

<div><em>Phytophthora cinnamomi</em> is a heterothallic, broad host range plant pathogen causing dieback and root rots of more than 3000 plant species. Several independent studies have suggested the existence of clonal lineages, primarily of the A2 mating type, and rarely sexual reproduction. However, a rigorous study of population diversity at a global scale is currently lacking. We analyzed 197 isolates of <em>P. cinnamomi</em> sampled from 11 countries. Genotyping by sequencing was performed using two restriction enzymes (PstI and MspI) and sequenced on the Illumina HiSeq 3000 platform. Raw reads were mapped to the <em>P. cinnamomi</em> reference genome using bowtie2 and variants were called with the GATK HaplotypeCaller. We tested the hypothesis of clonal reproduction in <em>P. cinnamomi </em>populations. A neighbor-joining tree based on 1,027 variants indicated that populations of <em>P. cinnamomi </em>from Southeast Asia (Taiwan & Vietnam) consisting of A1 and A2 mating type isolates were highly diverse whereas most isolates from the remaining countries formed two distinct clonal lineages of the A2 mating type. A1 mating type isolates from Papua New Guinea, South Africa and Australia grouped within the diverse Taiwanese and Vietnamese populations which were inferred to be partially sexual based on the index of association. This suggests that Southeast Asia might be a candidate center of origin for <em>P. cinnamomi</em> as speculated previously. These results provide novel insights into the existence of both mating types in Southeast Asia and probably sexual reproduction that could potentially give rise to novel aggressive genotypes or lineages.</div>