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      Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology

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          Abstract

          Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.

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          Most cited references17

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          Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen.

          Phytophthora infestans has been a named pathogen for well over 150 years and yet it continues to "emerge", with thousands of articles published each year on it and the late blight disease that it causes. This review explores five attributes of this oomycete pathogen that maintain this constant attention. First, the historical tragedy associated with this disease (Irish potato famine) causes many people to be fascinated with the pathogen. Current technology now enables investigators to answer some questions of historical significance. Second, the devastation caused by the pathogen continues to appear in surprising new locations or with surprising new intensity. Third, populations of P. infestans worldwide are in flux, with changes that have major implications to disease management. Fourth, the genomics revolution has enabled investigators to make tremendous progress in terms of understanding the molecular biology (especially the pathogenicity) of P. infestans. Fifth, there remain many compelling unanswered questions.
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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 a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor's G or Shannon and Wiener's H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.
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              The population genetics of phytophthora.

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                3 November 2016
                2016
                : 11
                : 11
                : e0165690
                Affiliations
                [1 ]Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, United States of America
                [2 ]Department of Plant Science and Landscape Architecture, University of Maryland, Salisbury, MD, United States of America
                [3 ]Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
                [4 ]Department of Plant Pathology, University of Wisconsin, Madison, WI, United States of America
                [5 ]Horticultural Crops Research Laboratory, United States Department of Agriculture–Agricultural Research Service, Corvallis, OR, United States of America
                [6 ]Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
                [7 ]Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
                [8 ]University of Maine Cooperative Extension, Presque Isle, ME, United States of America
                [9 ]Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, CA, United States of America
                [10 ]Plant Pathology and Plant-Microbe Biology Section, Cornell University, Riverhead, NY, United States of America
                [11 ]Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
                [12 ]Department of Plant Pathology, University of Florida, Immokalee, FL, United States of America
                [13 ]Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America
                Agriculture and Agri-Food Canada, CANADA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: ZRH NJG HSJ CDS.

                • Data curation: ZRH.

                • Formal analysis: ZRH.

                • Funding acquisition: HSJ ZRH CDS.

                • Investigation: ZRH CDS.

                • Methodology: ZRH CDS.

                • Resources: ZRH KLE WEF AJG NJG BKG DAJ SBJ HSJ MTM KLM JBR PDR GAS CDS.

                • Software: ZRH NJG BJK.

                • Validation: NJG BJK.

                • Visualization: ZRH.

                • Writing – original draft: ZRH.

                • Writing – review & editing: ZRH NJG HSJ CDS.

                Article
                PONE-D-16-23579
                10.1371/journal.pone.0165690
                5094694
                27812174
                0f9e171d-f460-482a-b44b-b809391a81fe

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 12 June 2016
                : 17 October 2016
                Page count
                Figures: 8, Tables: 1, Pages: 22
                Funding
                Funded by: USDA NIFA
                Award ID: 2011-68004-30154
                Award Recipient :
                Funded by: USDA NIFA
                Award ID: 2016-67011-25176
                Award Recipient :
                Funding for this work was provided by the United States Department of Agriculture, National Institute of Food and Agriculture Grant no. 2011-68004-30154. Additional support for Z. R. Hansen was provided by the United States Department of Agriculture, National Institute of Food and Agriculture Pre-Doctoral Fellowship no. 2016-67011-25176.
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                Custom metadata
                Data are linked to Bioproject PRJNA323952 and are available from the National Center for Biotechnology Information Short Read Archive (Accession Numbers SAMN05192735, SAMN05192831, and SAMN05192927).

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