{"id":9756,"date":"2019-05-21T12:43:19","date_gmt":"2019-05-21T12:43:19","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9756"},"modified":"2019-05-21T12:43:21","modified_gmt":"2019-05-21T12:43:21","slug":"article-journal-of-ecology-3","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9756","title":{"rendered":"Article: Journal of Ecology"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/S1754504818302800\">Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline <\/a>C Pauvert, M Bu\u00e9e, V Laval, V Edel-Hermann\u2026\u00a0&#8211; Fungal Ecology, 2019<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Abstract<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Fungal communities\u00a0associated with\u00a0plants\u00a0and\u00a0soilinfluence plant fitness and\u00a0ecosystem\u00a0functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal\u00a0internal transcribed spacer\u00a0(ITS), but there is no\u00a0consensusconcerning the most appropriate\u00a0bioinformaticapproach for the analysis of these data. We sequenced an artificial fungal community composed of 189\u00a0strainscovering a wide range of\u00a0Ascomycota\u00a0and\u00a0Basidiomycota, to compare the performance of 360\u00a0software\u00a0and parameter combinations. The most sensitive approaches, based on the USEARCH and VSEARCH\u00a0clustering\u00a0algorithms, detected almost all\u00a0fungal strains\u00a0but greatly overestimated the total number of strains. By\u00a0contrast, approaches using DADA2 to detect\u00a0amplicon\u00a0sequence variants were the most effective for recovering the richness and composition of the fungal community. Our results suggest that analyzing single forward (R1) sequences with DADA2 and no\u00a0filter\u00a0other than the removal of low-quality and chimeric sequences is a good option for fungal community characterization.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline C Pauvert, M Bu\u00e9e, V Laval, V Edel-Hermann\u2026\u00a0&#8211; Fungal Ecology, 2019 Abstract Fungal communities\u00a0associated with\u00a0plants\u00a0and\u00a0soilinfluence plant fitness and\u00a0ecosystem\u00a0functioning. They are frequently studied &hellip; <a href=\"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=9756\">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":[1],"tags":[],"class_list":["post-9756","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/9756","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=9756"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/9756\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9756"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9756"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9756"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}