{"id":9556,"date":"2019-03-13T14:26:24","date_gmt":"2019-03-13T14:26:24","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9556"},"modified":"2019-03-13T14:26:45","modified_gmt":"2019-03-13T14:26:45","slug":"article-journal-of-plant-pathology","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9556","title":{"rendered":"Article: Journal of Plant Pathology"},"content":{"rendered":"<p><a class=\"gsc_a_at\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s42161-019-00276-9\" data-href=\"\/citations?view_op=view_citation&amp;hl=fr&amp;user=WXK9kwwAAAAJ&amp;sortby=pubdate&amp;citation_for_view=WXK9kwwAAAAJ:738O_yMBCRsC\">Comparison and validation of Oomycetes metabarcoding primers for <i>Phytophthora<\/i> high throughput sequencing\u00a0<\/a>J Legeay, C Husson, T Cordier, C Vacher, B Marcais, M Bu\u00e9e Journal of Plant Pathology, 1-6<\/p>\n<h2 class=\"Heading\">Abstract<\/h2>\n<p id=\"Par1\" class=\"Para\" style=\"text-align: justify;\">Oomycetes are eukaryotic plant pathogens that require health monitoring. High-throughput sequencing (HTS) methods replace progressively cultivation-based approaches in soil surveys of Oomycetes, but very little control has been done from synthetic communities. Indeed, several potential biases do exist and need to be assessed for Oomycetes communities. We created a mock community by mixing DNA from 24 <em class=\"EmphasisTypeItalic \">Phytophthora<\/em> species. We amplified two barcode regions with Oomycete-specific primers before HTS. With this aim, we used three primer sets in nested PCR amplification, targeting the ITS-1 region or the RAS gene region. The three nested PCR strategies proved to be a reliable qualitative approach, identifying approximately 95% of the species after Illumina Miseq sequencing and bioinformatic analysis. However, quantitative proportions of each species showed distortions compared to the original mixture of the mock. In addition, we compared the two ITS primer sets on soil environmental DNA sampled from temperate forests. The \u2018oom18S-ITS7\/18ph2f-5.8S-1R\u2019 primer set, more specific to <em class=\"EmphasisTypeItalic \">Phytophthora<\/em>, was able to detect seven <em class=\"EmphasisTypeItalic \">Phytophthora<\/em> species, confirming what was expected for temperate forests. Using the \u2018DC6-ITS7\/oom18S-ITS7\u2019 primer set that covers the broader Peronosporaceans, we detected only one <em class=\"EmphasisTypeItalic \">Phytophthora<\/em> species among the dominance of <em class=\"EmphasisTypeItalic \">Pythium<\/em> and <em class=\"EmphasisTypeItalic \">Phytopythium<\/em> species. We concluded that \u2018oom18S-ITS7\/18ph2f-5.8S-1R\u2019 primer set is a reliable tool for the qualitative description of environmental <em class=\"EmphasisTypeItalic \">Phytophthora<\/em>communities.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing\u00a0J Legeay, C Husson, T Cordier, C Vacher, B Marcais, M Bu\u00e9e Journal of Plant Pathology, 1-6 Abstract Oomycetes are eukaryotic plant pathogens that require health monitoring. High-throughput sequencing &hellip; <a href=\"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9556\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[],"class_list":["post-9556","post","type-post","status-publish","format-standard","hentry","category-academic-productions"],"_links":{"self":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/9556","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=9556"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/9556\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9556"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9556"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9556"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}