Genetic analysis of field populations of the plant pathogens <i>Cercospora sojina</i>, <i>Corynespora cassiicola</i> and <i>Phytophthora colocasiae</i>

Genetic markers and whole genome sequencing (WGS) were used to study the disease dynamics and population structure for three important plant pathogens; Cercospora sojina (frogeye leaf spot of soybean), Corynespora cassiicola (target spot of soybean, cotton and many other crops) and Phytophthora colocasiae (taro leaf blight). For each pathogen, genome sequencing was used to guide the development of single nucleotide polymorphism (SNP) markers and both were used to investigate diversity in field populations. Investigation of C. sojina in Tennessee included comparisons of extant populations and historical isolates, revealing a dominant, potentially long-lived, clonal lineage. Characterization of QoI fungicide resistance indicates populations have adapted rapidly and that sexual recombination and heteroplasmy may play a role. Genome comparison of isolates of C. cassiicola from cotton and soybean indicates isolates from Tennessee are very similar but significantly different from an isolate recovered from rubber and that a revision of the species may be necessary. Genotype analyses of isolates of C. cassiicola from five southern US states indicates populations are dominated by a single clonal lineage. Genome sequencing and SNP genotyping for P. colocasiae recovered from Hawaii, Vietnam, China and Nepal revealed both inter- and intra-genomic variation in ploidy and a long-lived clonal population on the islands of Hawaii. This is the first report of intra-genomic ploidy variation within Phytophthora and the implications for evolution, adaptation and research are discussed.