Detecting unknown sequences with DNA microarrays: explorative probe design strategies
Identifieur interne : 000612 ( Istex/Corpus ); précédent : 000611; suivant : 000613Detecting unknown sequences with DNA microarrays: explorative probe design strategies
Auteurs : Eric Dugat-Bony ; Eric Peyretaillade ; Nicolas Parisot ; Corinne Biderre-Petit ; Faouzi Jaziri ; David Hill ; Sébastien Rimour ; Pierre PeyretSource :
- Environmental Microbiology [ 1462-2912 ] ; 2012-02.
Abstract
Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next‐generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high‐density microarray formats.
Url:
DOI: 10.1111/j.1462-2920.2011.02559.x
Links to Exploration step
ISTEX:A2A4DD88B03CB9CD6458E8297C28673DE944A343Le document en format XML
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F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation></author><author><name sortKey="Peyretaillade, Eric" sort="Peyretaillade, Eric" uniqKey="Peyretaillade E" first="Eric" last="Peyretaillade">Eric Peyretaillade</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation></author><author><name sortKey="Parisot, Nicolas" sort="Parisot, Nicolas" uniqKey="Parisot N" first="Nicolas" last="Parisot">Nicolas Parisot</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation></author><author><name sortKey="Biderre Etit, Corinne" sort="Biderre Etit, Corinne" uniqKey="Biderre Etit C" first="Corinne" last="Biderre-Petit">Corinne Biderre-Petit</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation></author><author><name sortKey="Jaziri, Faouzi" sort="Jaziri, Faouzi" uniqKey="Jaziri F" first="Faouzi" last="Jaziri">Faouzi Jaziri</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, LIMOS, BP 10448, F‐63000 Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</mods:affiliation></affiliation></author><author><name sortKey="Hill, David" sort="Hill, David" uniqKey="Hill D" first="David" last="Hill">David Hill</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, LIMOS, BP 10448, F‐63000 Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</mods:affiliation></affiliation></author><author><name sortKey="Rimour, Sebastien" sort="Rimour, Sebastien" uniqKey="Rimour S" first="Sébastien" last="Rimour">Sébastien Rimour</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation></author><author><name sortKey="Peyret, Pierre" sort="Peyret, Pierre" uniqKey="Peyret P" first="Pierre" last="Peyret">Pierre Peyret</name><affiliation><mods:affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</mods:affiliation></affiliation><affiliation><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: pierre.peyret@univ‐bpclermont.fr</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Environmental Microbiology</title><title level="j" type="sub">Taxonomy and Biodiversity</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><biblScope unit="vol">14</biblScope><biblScope 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type="first">Eric</forename><surname>Dugat‐Bony</surname></persName><affiliation><orgName type="institution">Clermont Université</orgName><orgName type="institution">Université Blaise Pascal</orgName><orgName type="laboratory">Laboratoire Microorganismes: Génome et Environnement</orgName><address><addrLine>BP 10448</addrLine><addrLine>F‐63000, Clermont‐Ferrand</addrLine></address></affiliation><affiliation><address><addrLine>UMR CNRS 6023</addrLine><addrLine>Université Blaise Pascal, 63000 Clermont‐Ferrand, France</addrLine><country key="FR" xml:lang="en">FRANCE</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Eric</forename><surname>Peyretaillade</surname></persName><affiliation><orgName type="institution">Clermont Université</orgName><orgName type="institution">Université Blaise Pascal</orgName><orgName type="laboratory">Laboratoire Microorganismes: Génome et Environnement</orgName><address><addrLine>BP 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E‐mail <email normalForm="pierre.peyret@univ-bpclermont.fr">pierre.peyret@univ‐bpclermont.fr</email>; Tel. (+33) 473405139; Fax (+33) 473407670.
</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:EMI.EMI2559.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 31 March, 2011; accepted 4 July, 2011.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="3"></count><count type="tableTotal" number="3"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="139"></count><count type="wordTotal" number="11311"></count><count type="linksPubMed" number="0"></count><count type="linksCrossRef" number="0"></count></countGroup><titleGroup><title type="main">Detecting unknown sequences with DNA microarrays: explorative probe design strategies</title><title type="shortAuthors">E. Dugat‐Bony <i>et al</i>.</title><title type="short">Explorative probes for environmental microarrays</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1 #a2"><personName><givenNames>Eric</givenNames><familyName>Dugat‐Bony</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1 #a2"><personName><givenNames>Eric</givenNames><familyName>Peyretaillade</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1 #a2"><personName><givenNames>Nicolas</givenNames><familyName>Parisot</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1 #a2"><personName><givenNames>Corinne</givenNames><familyName>Biderre‐Petit</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a3 #a4"><personName><givenNames>Faouzi</givenNames><familyName>Jaziri</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a3 #a4"><personName><givenNames>David</givenNames><familyName>Hill</familyName></personName></creator><creator creatorRole="author" xml:id="cr7" affiliationRef="#a1 #a2"><personName><givenNames>Sébastien</givenNames><familyName>Rimour</familyName></personName></creator><creator creatorRole="author" xml:id="cr8" affiliationRef="#a1 #a2" corresponding="yes"><personName><givenNames>Pierre</givenNames><familyName>Peyret</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1"><unparsedAffiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="FR"><unparsedAffiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</unparsedAffiliation></affiliation><affiliation xml:id="a3"><unparsedAffiliation>Clermont Université, Université Blaise Pascal, LIMOS, BP 10448, F‐63000 Clermont‐Ferrand</unparsedAffiliation></affiliation><affiliation xml:id="a4"><unparsedAffiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</unparsedAffiliation></affiliation></affiliationGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next‐generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high‐density microarray formats.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Detecting unknown sequences with DNA microarrays: explorative probe design strategies</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Explorative probes for environmental microarrays</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Detecting unknown sequences with DNA microarrays: explorative probe design strategies</title></titleInfo><name type="personal"><namePart type="given">Eric</namePart><namePart type="family">Dugat‐Bony</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Eric</namePart><namePart type="family">Peyretaillade</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nicolas</namePart><namePart type="family">Parisot</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Corinne</namePart><namePart type="family">Biderre‐Petit</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Faouzi</namePart><namePart type="family">Jaziri</namePart><affiliation>Clermont Université, Université Blaise Pascal, LIMOS, BP 10448, F‐63000 Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David</namePart><namePart type="family">Hill</namePart><affiliation>Clermont Université, Université Blaise Pascal, LIMOS, BP 10448, F‐63000 Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Sébastien</namePart><namePart type="family">Rimour</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Pierre</namePart><namePart type="family">Peyret</namePart><affiliation>Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement, BP 10448, F‐63000, Clermont‐Ferrand</affiliation><affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</affiliation><affiliation>E-mail: pierre.peyret@univ‐bpclermont.fr</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="reviewArticle" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-02</dateIssued><edition>Received 31 March, 2011; accepted 4 July, 2011.</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">3</extent><extent unit="tables">3</extent><extent unit="formulas">0</extent><extent unit="references">139</extent><extent unit="linksCrossRef">0</extent><extent unit="words">11311</extent></physicalDescription><abstract lang="en">Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next‐generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. 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