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Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, fewExpand
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brownExpand
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Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality
To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations isExpand
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Analysis of genotypic diversity data for populations of microorganisms.
ABSTRACT Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are aExpand
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Emergence of the sudden oak death pathogen Phytophthora ramorum.
The recently emerged plant pathogen Phytophthora ramorum is responsible for causing the sudden oak death epidemic. This review documents the emergence of P. ramorum based on evolutionary andExpand
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Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen
Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, PhytophthoraExpand
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New Populations of Sclerotinia sclerotiorum from Lettuce in California and Peas and Lentils in Washington.
ABSTRACT Four populations of Sclerotinia sclerotiorum in North America were inferred previously, based on analyses of both rapidly evolving markers (DNA fingerprint and mycelial compatiblity), andExpand
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Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004
Phytophthora ramorum (Oomycetes) is an emerging plant pathogen in forests in southwestern Oregon (Curry County). Moreover, since 2003 it has been repeatedly isolated from plants in Oregon nurseries.Expand
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Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
TLDR
We developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data and community visualization in R. Expand
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Population Genetic Analysis Infers Migration Pathways of Phytophthora ramorum in US Nurseries
Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can revealExpand
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