{"id":4738,"date":"2015-02-22T18:34:08","date_gmt":"2015-02-22T18:34:08","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4738"},"modified":"2015-02-22T18:37:56","modified_gmt":"2015-02-22T18:37:56","slug":"article-molecular-ecology-resources","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4738","title":{"rendered":"Article: Molecular Ecology Resources"},"content":{"rendered":"<p><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.12391\/abstract\" shape=\"rect\">A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the P\u00e9rigord black truffle (<em>Tuber melanosporum<\/em>\u00a0Vittad.)<\/a><\/p>\n<p style=\"text-align: justify;\">Thibaut Payen, Claude Murat, Ana\u00efs Gigant, Emmanuelle Morin, St\u00e9phane De Mita and Francis Martin<\/p>\n<h3 style=\"text-align: justify;\"><strong>Abstract<\/strong><\/h3>\n<div class=\"para\">\n<p style=\"text-align: justify;\">The P\u00e9rigord black truffle (<em>Tuber melanosporum<\/em>\u00a0Vittad.), considered a gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus that is ecologically important in Mediterranean French, Italian, and Spanish woodlands. In this study, we developed a novel resource of single nucleotide polymorphisms (SNPs) for\u00a0<em>T. melanosporum<\/em>\u00a0using Illumina high-throughput re-sequencing. The genome from six\u00a0<em>T. melanosporum<\/em>\u00a0geographic accessions was sequenced to a depth of ~20\u00d7. These geographic accessions were selected from different populations within the northern and southern regions of the geographical species distribution. Approximately 80% of the reads for each of the six re-sequenced geographic accessions mapped against the reference\u00a0<em>T. melanosporum<\/em>\u00a0genome assembly, estimating the core genome size of this organism to be ~110 Mbp. A total of 442,326 SNPs corresponding to 3,540 SNPs\/Mbps were identified as being included in all seven genomes. The SNPs occurred more frequently in repeated sequences (85%), although 4,501 SNPs were also identified in the coding regions of 2,587 genes. Using the ratio of non-synonymous mutations per non-synonymous site (pN) to synonymous mutations per synonymous site (pS) and Tajima&#8217;s D index scanning the whole genome, we were able to identify genomic regions and genes potentially subjected to positive or purifying selection. The SNPs identified represent a valuable resource for future population genetics and genomics studies.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the P\u00e9rigord black truffle (Tuber melanosporum\u00a0Vittad.) Thibaut Payen, Claude Murat, Ana\u00efs Gigant, Emmanuelle Morin, St\u00e9phane De Mita and Francis Martin Abstract The P\u00e9rigord black truffle (Tuber melanosporum\u00a0Vittad.), considered a &hellip; <a href=\"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=4738\">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-4738","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\/4738","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=4738"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/4738\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4738"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4738"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4738"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}