Detecting unknown sequences with DNA microarrays: explorative probe design strategies
Identifieur interne : 000612 ( Istex/Curation ); précédent : 000611; suivant : 000613Detecting unknown sequences with DNA microarrays: explorative probe design strategies
Auteurs : Eric Dugat-Bony [France] ; Eric Peyretaillade [France] ; Nicolas Parisot [France] ; Corinne Biderre-Petit [France] ; Faouzi Jaziri ; David Hill ; Sébastien Rimour [France] ; Pierre Peyret [France]Source :
- 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.
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DOI: 10.1111/j.1462-2920.2011.02559.x
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Faouzi Jaziri<affiliation><mods:affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</mods:affiliation><wicri:noCountry code="subField">Aubière.</wicri:noCountry></affiliation><affiliation><mods:affiliation>UMR CNRS 6158, LIMOS, F‐63173 Aubière.</mods:affiliation><wicri:noCountry code="subField">Aubière.</wicri:noCountry></affiliation>Le document en format XML
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6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></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 wicri:level="1"><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></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 wicri:level="1"><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></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 wicri:level="1"><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></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><wicri:noCountry code="subField">Aubière.</wicri:noCountry></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><wicri:noCountry code="subField">Aubière.</wicri:noCountry></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 wicri:level="1"><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></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 wicri:level="1"><mods:affiliation>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand, France</mods:affiliation><country xml:lang="fr">France</country><wicri:regionArea>UMR CNRS 6023, Université Blaise Pascal, 63000 Clermont‐Ferrand</wicri:regionArea></affiliation><affiliation wicri:level="1"><mods:affiliation>E-mail: pierre.peyret@univ‐bpclermont.fr</mods:affiliation><country wicri:rule="url">France</country></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 unit="issue">2</biblScope><biblScope unit="page" from="356">356</biblScope><biblScope unit="page" to="371">371</biblScope><biblScope unit="page-count">16</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-02">2012-02</date></imprint><idno type="ISSN">1462-2912</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml: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. Finally, these innovative probe design approaches require exploiting newly available high‐density microarray formats.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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