Analysis of plant microbe interactions in the era of next generation sequencing technologies
Identifieur interne : 000531 ( Ncbi/Merge ); précédent : 000530; suivant : 000532Analysis of plant microbe interactions in the era of next generation sequencing technologies
Auteurs : Claudia KniefSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2014.
Abstract
Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.
Url:
DOI: 10.3389/fpls.2014.00216
PubMed: 24904612
PubMed Central: 4033234
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<front><div type="abstract" xml:lang="en"><p>Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.</p>
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<pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id>
<journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title-group><journal-title>Frontiers in Plant Science</journal-title>
</journal-title-group>
<issn pub-type="epub">1664-462X</issn>
<publisher><publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24904612</article-id>
<article-id pub-id-type="pmc">4033234</article-id>
<article-id pub-id-type="doi">10.3389/fpls.2014.00216</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject>
<subj-group><subject>Review Article</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Analysis of plant microbe interactions in the era of next generation sequencing technologies</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Knief</surname>
<given-names>Claudia</given-names>
</name>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/22515"></uri>
</contrib>
</contrib-group>
<aff><institution>Institute of Crop Science and Resource Conservation—Molecular Biology of the Rhizosphere, Faculty of Agriculture, University of Bonn</institution>
<country>Bonn, Germany</country>
</aff>
<author-notes><fn fn-type="edited-by"><p>Edited by: Ann E. Stapleton, University of North Carolina Wilmington, USA</p>
</fn>
<fn fn-type="edited-by"><p>Reviewed by: Xingyi Guo, Albert Einstein College of Medicine, USA; Ute Hentschel, University of Wuerzburg, Germany</p>
</fn>
<corresp id="fn001">*Correspondence: Claudia Knief, Institute of Crop Science and Resource Conservation–Molecular Biology of the Rhizosphere, Faculty of Agriculture, Nussallee 13, 53115 Bonn, Germany e-mail: <email xlink:type="simple">knief@uni-bonn.de</email>
</corresp>
<fn fn-type="other" id="fn002"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science.</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>21</day>
<month>5</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<volume>5</volume>
<elocation-id>216</elocation-id>
<history><date date-type="received"><day>15</day>
<month>2</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>30</day>
<month>4</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Knief.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p>
</license>
</permissions>
<abstract><p>Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.</p>
</abstract>
<kwd-group><kwd>next generation sequencing</kwd>
<kwd>plant microbiota</kwd>
<kwd>phyllosphere</kwd>
<kwd>rhizosphere</kwd>
<kwd>metagenomics</kwd>
<kwd>amplicon sequencing</kwd>
</kwd-group>
<counts><fig-count count="2"></fig-count>
<table-count count="3"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="232"></ref-count>
<page-count count="23"></page-count>
<word-count count="21245"></word-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Knief, Claudia" sort="Knief, Claudia" uniqKey="Knief C" first="Claudia" last="Knief">Claudia Knief</name>
</noCountry>
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</record>
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