{"id":2799,"date":"2018-04-04T12:00:47","date_gmt":"2018-04-04T10:00:47","guid":{"rendered":"https:\/\/ist.blogs.inra.fr\/afs\/?p=2799"},"modified":"2018-06-22T11:21:53","modified_gmt":"2018-06-22T09:21:53","slug":"rapid-and-economical-protocols-for-genomic-and-metagenomic-dna-extraction-from-oak-quercus-brantii-lindl","status":"publish","type":"post","link":"https:\/\/ist.blogs.inrae.fr\/afs\/2018\/04\/04\/rapid-and-economical-protocols-for-genomic-and-metagenomic-dna-extraction-from-oak-quercus-brantii-lindl\/","title":{"rendered":"Rapid and economical protocols for genomic and metagenomic DNA extraction from oak (Quercus brantii Lindl.)"},"content":{"rendered":"<script type='text\/javascript' src='https:\/\/d1bxh8uas1mnw7.cloudfront.net\/assets\/embed.js'><\/script><p><a href=\"https:\/\/ist.blogs.inra.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2800 alignleft\" src=\"https:\/\/ist.blogs.inra.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018-300x162.png\" alt=\"\" width=\"300\" height=\"162\" srcset=\"https:\/\/ist.blogs.inrae.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018-300x162.png 300w, https:\/\/ist.blogs.inrae.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018-768x414.png 768w, https:\/\/ist.blogs.inrae.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018-1024x552.png 1024w, https:\/\/ist.blogs.inrae.fr\/afs\/wp-content\/uploads\/sites\/5\/2018\/04\/Ahmadi2018.png 1226w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a>Two new efficient, fast and low-cost metagenomic DNA extraction methods were developed for different Persian oak tissues (leaf, stem, root, and rhizospheric) and soil samples.<\/p>\n<p><strong>Context<\/strong> The new \u201comics\u201d studies on the genus <em>Quercus<\/em> are of importance to help finding efficient strategies for overcoming environmental challenges, and to do this, presence of efficient DNA extraction protocols for different <em>Quercus<\/em> species are very critical.<br \/>\n<strong>Aims<\/strong> The objective of the present study was to develop new efficient methods for extraction of metagenomic DNA (mDNA) from of Persian oak (<em>Quercus brantii<\/em> Lindl.) tissues.<br \/>\n<strong>Methods<\/strong> The efficiency of two newly developed mDNA extraction methods, including indirect SDS-based (ISB or concentrate method) and one spin column-based method (SCB) were compared to that of two classical direct methods, including CTAB-based and SDS-based methods, and two commercial mDNA extraction kits.<br \/>\n<strong>Results<\/strong> The maximum average yield of mDNA for all samples (leaf, stem, root, bulk, and rhizospheric soils) was obtained by SCB (258 ng\/\u03bcl) and ISB (189 ng\/\u03bcl) methods, respectively. Successful PCR amplification for 16SrRNA and ITS sequence was consistently observed for ISB, SCB, and kit-extracted mDNAs, which confirmed the high purity of mDNA extracted by these methods. The new methods showed more than 96% quantitative PCR efficiency, and partial restriction digestion and metagenomic library construction confirmed the high efficiency of the newly developed methods.<br \/>\n<strong>Conclusion<\/strong> It could be concluded that two new protocols enhanced efficiency (yield, purity, and cost) of mDNA extraction from different tissues of Persian oak.<\/p>\n<p>Keywords<br \/>\nIndirect SDS-based method (ISB), Metagenomic DNA extraction, Microbiome, Oak decline, <em>Quercus brantii<\/em>, Spin column-based method (SCB)<\/p>\n<div class='altmetric-embed' data-badge-type='donut' data-doi='10.1007\/s13595-018-0705-y'  style='float: right; ' ><\/div>\n<p>Publication<br \/>\nAhmadi, E., Kowsari, M., Azadfar, D. et al. Annals of Forest Science (2018) 75: 43. <a href=\"https:\/\/doi.org\/10.1007\/s13595-018-0705-y\">https:\/\/doi.org\/10.1007\/s13595-018-0705-y<\/a><\/p>\n<p>For the read-only version of the full text: <a href=\"https:\/\/rdcu.be\/KA9l\">https:\/\/rdcu.be\/KA9l<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Two new efficient, fast and low-cost metagenomic DNA extraction methods were developed for different Persian oak tissues (leaf, stem, root, and rhizospheric) and soil samples. Context The new \u201comics\u201d studies on the genus Quercus are of importance to help finding efficient strategies for overcoming environmental challenges, and to do this, presence of efficient DNA extraction [&hellip;]<\/p>\n","protected":false},"author":94,"featured_media":2804,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[14,15],"tags":[],"class_list":["post-2799","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-article-type","category-research-paper","cat-14-id","cat-15-id","has_thumb"],"_links":{"self":[{"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/posts\/2799","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/users\/94"}],"replies":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/comments?post=2799"}],"version-history":[{"count":0,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/posts\/2799\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/media\/2804"}],"wp:attachment":[{"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/media?parent=2799"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/categories?post=2799"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/afs\/wp-json\/wp\/v2\/tags?post=2799"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}