Abstract
BackgroundMembers of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.ResultsThe number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.ConclusionIn all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.
Highlights
Members of the genus Phytophthora are notorious pathogens with world-wide distribution
Microsatellites: motif, length and frequency Consensus Expressed Sequence Tag. simple sequence repeats (SSRs) (EST) databases from P. infestans and annotated transcripts from P. sojae and P. ramorum, were scanned for the presence of microsatellites, defined as short tandem
A total of 84000 available EST sequences were downloaded from the Phytophthora Functional Genomics Database [31] for P. infestans, and 19276 and 16066 predicted and annotated transcripts were downloaded from the Department of Energy's Joint Genome Institute [32]
Summary
Members of the genus Phytophthora are notorious pathogens with world-wide distribution. Phytophthora spp. are notorious, world-wide pathogens because of their devastating effects on many crop species, that often result in significant economic losses. P. ramorum has only been described relatively recently, so that basic information about its biology and ecology is scant. This pathogen causes sudden oak death disease and is currently decimating trees and shrubs in the coastal oak forest in California, including keystone tanoak and coast live oak species, and might be expanding to other hosts such as redwoods and to other regions in North America [6]
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