Resequencing of the Phytophthora ramorum genome to characterize genetic variation and population dynamics of the invasive pathogen
| Authors: | Jennifer Yuzon, David M. Rizzo, Mathu Malar C, Sucheta Tripathy, Takao Kasuga |
| Year: | 2017 |
| Type: | General Technical Report |
| Station: | Pacific Southwest Research Station |
| Source: | Proceedings of the sudden oak death sixth science symposium. Gen. Tech. Rep. GTR-PSW-255. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station: 105-106. |
Abstract
Phytophthora ramorum has spread and diversified throughout California’s northwestern coast since its introduction in the 1990s. Tracking the spread of P. ramorum and the functional response of the pathogen to the environment is of particular interest to managing the epidemic. Using genetic tools such as microsatellite markers, researchers have learned much of the pathogen’s epidemiology by identifying migrational pathways and new introductions. However, higher resolution markers may reveal previously undetected substructure.
Work at the genetic and genomic level is underway to identify markers in the form of single nucleotide polymorphisms (SNPs), not only for a higher resolution of population structure, but to identify genetic responses of the pathogen to its adopted environment. Because SNPs are more common throughout the genome and have a lower likelihood of violating the infinite sites assumption, a genome-wide SNP dataset will help reconstruct the evolutionary past of P. ramorum; identify fitness and selection for genes; and possibly associate population subdivision based on geography, climate, or other influences on population dynamics. Structural variants and chromosomal abnormalities are also of interest because such genetic variation can add another layer of evolutionary potential for the rapidly expanding population.