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United States Department of Agriculture

Agricultural Research Service

Research Project: Detection and Management of Pathogens in Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora

Authors
item MARTIN, FRANK
item Blair, Jaime -
item Coffey, Mike -

Submitted to: Fungal Genetics and Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 24, 2014
Publication Date: April 12, 2014
Citation: Martin, F.N., Blair, J.E., Coffey, M.D. 2014. A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora. Fungal Genetics and Biology. 66:19-32.

Interpretive Summary: The number of described species in the plant pathogen genus Phytophthora has essentially doubled in the past 10 years. DNA sequence data from nuclear genes collected from a prior study was combined with mitochondrial gene data from the same isolates to provide a more comprehensive evaluation of evolutionary relationships among species. Additional more recently described species were also included in the analysis.

Technical Abstract: The most recent phylogenetic analysis of the genus Phytophthora was completed in 2008 (Blair et al. 2008) and utilized 8.1 kb of sequence data from seven nuclear loci. Given the large number of species that have recently been described, this study was undertaken to broaden the available information on the phylogeny of the genus. A total of 166 isolates representing 90 recognized species and 17 provisional species were analyzed here, including many of the same isolates used in the nuclear multilocus study of Blair et al. (2008). Four mitochondrial genes (cox2, nad9, rps10 and secY) were sequenced with a total of 2,373 bp used in the analysis; the species relationships recovered with mitochondrial data were largely consistent with those observed previously in the nuclear analysis. Combining the new mitochondrial data with the nuclear data from Blair et al. (2008) generated a dataset of 10,828 bp representing 11 loci, however resolution of clade relationships was still low. We therefore implemented a modified multispecies coalescent approach with a subset of the data, and recovered increased resolution and moderate to high support for clade relationships. A more detailed analysis of species from clades 2 and 8 identified an additional seven phylogenetic lineages that warrant further investigation to determine if they represent distinct species. As has been reported in other phylogenetic studies of the genus, there is no consistent correlation between phylogenetic relatedness and morphological features or ecology.

Last Modified: 9/10/2014
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