Diversity and clonality in populations of Phytophthora citrophthora and P. syringae causing brown rot of citrus in California

Abstract

Phytophthora citrophthora and P. syringae are currently the primary causal organisms of brown rot of citrus fruits in California. To possibly find an explanation for the prevalence of the previously minor species P. syringae, we determined the population structures of both pathogens using next-generation sequencing and population genomics analyses. Whole genome sequencing and aligning with newly assembled reference genomes identified 972,266 variants in 132 isolates of P. citrophthora and 422,208 variants in 154 isolates (including 24 from non-citrus tree crops) of P. syringae originating from three major growing regions. Resulting data sets were visualized using principal component analysis, discriminant analysis of principal components, UPGMA dendrograms, fastStructure, and minimum spanning networks, and we obtained index of association, diversity summary statistics, and genetic distance statistics values GST, G”ST, and Jost’s D. Sub-populations of both species were mostly defined by geographic origin indicating restricted dispersal of inoculum. Except for five isolates, population structure of P. citrophthora (that is heterothallic and unlikely to reproduce sexually) was clonal to semi-clonal with very little genetic diversity within and among sub-groups. Population structure of the homothallic P. syringae was also clonal to semi-clonal, but isolates were placed into four main clusters of much higher diversity. Clonality in both species can be explained by high levels of asexual reproduction. The higher diversity in P. syringae is likely due to commonly occurring sexual reproduction. One distinct cluster of P. syringae consisted solely of isolates from non-citrus hosts; therefore, the origin of P. syringae in citrus could not be resolved.