Soilborne with an Aerial Habitat: Characterization of \u3cem\u3ePhytophthora\u3c/em\u3e Species Recovered from Nursery and Vegetable Production in Tennessee

Molecular and morphological characterization of Phytopthora isolates recovered from Ericaceous nursery hosts throughout the state of Tennessee over two years allowed for the identification of six known species and one previously undescribed species. The undescribed species was observed in California and Tennessee simultaneously and a species description is provided for P. foliorum sp. nov. Of the six known species recovered from nursery hosts, P. citricola and P. citrophthora were recovered most frequently, exhibit diverse AFLP genotypes within the state, and are likely moved via the nursery trade. Other species recovered included P. cactorum, P. nicotianae, P. palmivora, and P. tropicalis. Upon the observation of both P. tropicalis from nursery hosts and P. capsici from vegetable hosts within the state interspecific crosses were performed between isolates from each species. Characterization of oospore progeny using AFLP and DNA sequence data from these crosses demonstrate that interspecific hybridization is possible. Additionally, apomixis or asexual reproduction via a sexual structure was observed in some crosses. Utility of AFLP markers used in these crosses quickly degraded. Upon these observations, a novel set of DNA-based markers were sought for use with laboratory crosses and field isolates. Using primary sequence data from the P. capsici genome sequencing project 36 loci were analyzed in a four isolate panel, plus one isolate of P. tropicalis. A subset of assays were developed using high-resolution DNA melting analysis. These assays were implemented in characterizing field isolates from one vegetable production facility over four years. The data suggests that the sexual stage and recomnbination is occurring in Tennessee vegetable fields infested with P. capsici

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici