A barcode-based phylogenetic characterization of Phytophthora cactorum identifies two cosmopolitan lineages with distinct host affinities and the first report of Phytophthora pseudotsugae in California
Fajardo, Sebastian N., University of California, Davis
Engert, Cole P., University of California, Davis
Rizzo, David M., University of California, Davis
tbbourret@ucdavis.edu
Published Jul 11, 2022 on Dryad.
https://doi.org/10.25338/B8J33M
Cite this dataset
Bourret, Tyler; Fajardo, Sebastian N.; Engert, Cole P.; Rizzo, David M. (2022). A barcode-based phylogenetic characterization of Phytophthora cactorum identifies two cosmopolitan lineages with distinct host affinities and the first report of Phytophthora pseudotsugae in California [Dataset]. Dryad. https://doi.org/10.25338/B8J33M
Abstract
A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade 1a) strains isolated from several recent surveys across California was phylogenetically compared to a worldwide collection of 112 conspecific strains using sequences from three barcoding loci. The surveys baited P. cactorum from soil and water across a wide variety of forested ecosystems with a geographic range of more than 1000 km. Two cosmopolitan lineages were identified within the widespread P. cactorum, one being mainly associated with strawberry production and the other more closely associated with apple orchards, oaks and ornamental trees. Two other well-sampled P. cactorum lineages, including one that dominated Californian restoration outplantings, were only found in the western United States, while a third was only found in Japan. Coastal California forest isolates of both Phytophthora species exhibited considerable diversity, suggesting both may be indigenous to the state. Many isolates with sequence accessions deposited as P. cactorum were determined to be P. hedraiandra and P. ×serendipita, with one hybrid lineage appearing relatively common across Europe and Asia. This study contains the first report of P. pseudotsugae from the state of California and one of the only reports of that species since its original description.
Methods
Sequences were derived by BLASTing a moving window of each locus against data in the sequence read archive corresponding to the listed BioSamples. Alignments are phylip files (.phy) and a nexus file (.nex) used as the input for IQTREE2.
Funding
USDA Forest Service, Forest Health Protection, Award: N/A
USDA Forest Service, Forest Health Protection, Award: N/A
USDA Forest Service, Forest Health Protection, Award: N/A
USDA Forest Service, Forest Health Protection, Award: N/A
USDA Forest Service, Forest Health Protection, Award: N/A
USDA Forest Service, Forest Health Protection, Award: N/A
