Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.
Identifieur interne : 000C45 ( Main/Exploration ); précédent : 000C44; suivant : 000C46Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.
Auteurs : Richard Sibout [France] ; Sebastian Proost [Allemagne] ; Bjoern Oest Hansen [Allemagne] ; Neha Vaid [Allemagne] ; Federico M. Giorgi [Royaume-Uni] ; Severine Ho-Yue-Kuang [France] ; Frédéric Legée [France] ; Laurent Cézart [France] ; Oumaya Bouchabké-Coussa [France] ; Camille Soulhat [France] ; Nicholas Provart [Canada] ; Asher Pasha [Canada] ; Philippe Le Bris [France] ; David Roujol [France] ; Herman Hofte [France] ; Elisabeth Jamet [France] ; Catherine Lapierre [France] ; Staffan Persson [Australie] ; Marek Mutwil [Allemagne]Source :
- The New phytologist [ 1469-8137 ] ; 2017.
Abstract
While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.
DOI: 10.1111/nph.14635
PubMed: 28617955
Affiliations:
- Allemagne, Australie, Canada, France, Royaume-Uni
- Brandebourg, Ontario, Victoria (État), Île-de-France
- Melbourne, Potsdam, Toronto
- Université de Melbourne, Université de Toronto
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Sibout</name><affiliation wicri:level="3"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Proost, Sebastian" sort="Proost, Sebastian" uniqKey="Proost S" first="Sebastian" last="Proost">Sebastian Proost</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476</wicri:regionArea><placeName><region type="land" nuts="2">Brandebourg</region><settlement type="city">Potsdam</settlement></placeName></affiliation></author><author><name sortKey="Hansen, Bjoern Oest" sort="Hansen, Bjoern Oest" uniqKey="Hansen B" first="Bjoern Oest" last="Hansen">Bjoern Oest Hansen</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476</wicri:regionArea><placeName><region type="land" nuts="2">Brandebourg</region><settlement type="city">Potsdam</settlement></placeName></affiliation></author><author><name sortKey="Vaid, Neha" sort="Vaid, Neha" uniqKey="Vaid N" first="Neha" last="Vaid">Neha Vaid</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476</wicri:regionArea><placeName><region type="land" nuts="2">Brandebourg</region><settlement type="city">Potsdam</settlement></placeName></affiliation></author><author><name sortKey="Giorgi, Federico M" sort="Giorgi, Federico M" uniqKey="Giorgi F" first="Federico M" last="Giorgi">Federico M. Giorgi</name><affiliation wicri:level="1"><nlm:affiliation>Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE</wicri:regionArea><wicri:noRegion>CB2 0RE</wicri:noRegion></affiliation></author><author><name sortKey="Ho Yue Kuang, Severine" sort="Ho Yue Kuang, Severine" uniqKey="Ho Yue Kuang S" first="Severine" last="Ho-Yue-Kuang">Severine Ho-Yue-Kuang</name><affiliation wicri:level="1"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><wicri:noRegion>78026</wicri:noRegion><wicri:noRegion>78026</wicri:noRegion></affiliation></author><author><name sortKey="Legee, Frederic" sort="Legee, Frederic" uniqKey="Legee F" first="Frédéric" last="Legée">Frédéric Legée</name><affiliation wicri:level="3"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><wicri:noRegion>78026</wicri:noRegion><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Cezart, Laurent" sort="Cezart, Laurent" uniqKey="Cezart L" first="Laurent" last="Cézart">Laurent Cézart</name><affiliation wicri:level="3"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Bouchabke Coussa, Oumaya" sort="Bouchabke Coussa, Oumaya" uniqKey="Bouchabke Coussa O" first="Oumaya" last="Bouchabké-Coussa">Oumaya Bouchabké-Coussa</name><affiliation wicri:level="3"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Soulhat, Camille" sort="Soulhat, Camille" uniqKey="Soulhat C" first="Camille" last="Soulhat">Camille Soulhat</name><affiliation wicri:level="3"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Provart, Nicholas" sort="Provart, Nicholas" uniqKey="Provart N" first="Nicholas" last="Provart">Nicholas Provart</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Pasha, Asher" sort="Pasha, Asher" uniqKey="Pasha A" first="Asher" last="Pasha">Asher Pasha</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Le Bris, Philippe" sort="Le Bris, Philippe" uniqKey="Le Bris P" first="Philippe" last="Le Bris">Philippe Le Bris</name><affiliation wicri:level="1"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><wicri:noRegion>78026</wicri:noRegion><wicri:noRegion>78026</wicri:noRegion></affiliation></author><author><name sortKey="Roujol, David" sort="Roujol, David" uniqKey="Roujol D" first="David" last="Roujol">David Roujol</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Hofte, Herman" sort="Hofte, Herman" uniqKey="Hofte H" first="Herman" last="Hofte">Herman Hofte</name><affiliation wicri:level="1"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><wicri:noRegion>78026</wicri:noRegion><wicri:noRegion>78026</wicri:noRegion></affiliation></author><author><name sortKey="Jamet, Elisabeth" sort="Jamet, Elisabeth" uniqKey="Jamet E" first="Elisabeth" last="Jamet">Elisabeth Jamet</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan</wicri:regionArea><wicri:noRegion>Castanet-Tolosan</wicri:noRegion><wicri:noRegion>Castanet-Tolosan</wicri:noRegion></affiliation></author><author><name sortKey="Lapierre, Catherine" sort="Lapierre, Catherine" uniqKey="Lapierre C" first="Catherine" last="Lapierre">Catherine Lapierre</name><affiliation wicri:level="1"><nlm:affiliation>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Jean-Pierre Bourgin, UMR 1318, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles Cedex, 78026</wicri:regionArea><wicri:noRegion>78026</wicri:noRegion><wicri:noRegion>78026</wicri:noRegion></affiliation></author><author><name sortKey="Persson, Staffan" sort="Persson, Staffan" uniqKey="Persson S" first="Staffan" last="Persson">Staffan Persson</name><affiliation wicri:level="4"><nlm:affiliation>School of Biosciences, University of Melbourne, Parkville, Vic., 3010, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Biosciences, University of Melbourne, Parkville, Vic., 3010</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Mutwil, Marek" sort="Mutwil, Marek" uniqKey="Mutwil M" first="Marek" last="Mutwil">Marek Mutwil</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476</wicri:regionArea><placeName><region type="land" nuts="2">Brandebourg</region><settlement type="city">Potsdam</settlement></placeName></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Australie</li><li>Canada</li><li>France</li><li>Royaume-Uni</li></country><region><li>Brandebourg</li><li>Ontario</li><li>Victoria (État)</li><li>Île-de-France</li></region><settlement><li>Melbourne</li><li>Potsdam</li><li>Toronto</li></settlement><orgName><li>Université de Melbourne</li><li>Université de Toronto</li></orgName></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Sibout, Richard" sort="Sibout, Richard" uniqKey="Sibout R" first="Richard" last="Sibout">Richard Sibout</name></region><name sortKey="Bouchabke Coussa, Oumaya" sort="Bouchabke Coussa, Oumaya" uniqKey="Bouchabke Coussa O" first="Oumaya" last="Bouchabké-Coussa">Oumaya Bouchabké-Coussa</name><name sortKey="Cezart, Laurent" sort="Cezart, Laurent" uniqKey="Cezart L" first="Laurent" last="Cézart">Laurent Cézart</name><name sortKey="Ho Yue Kuang, Severine" sort="Ho Yue Kuang, Severine" uniqKey="Ho Yue Kuang S" first="Severine" last="Ho-Yue-Kuang">Severine Ho-Yue-Kuang</name><name sortKey="Hofte, Herman" sort="Hofte, Herman" uniqKey="Hofte H" first="Herman" last="Hofte">Herman Hofte</name><name sortKey="Jamet, Elisabeth" sort="Jamet, Elisabeth" uniqKey="Jamet E" first="Elisabeth" last="Jamet">Elisabeth Jamet</name><name sortKey="Lapierre, Catherine" sort="Lapierre, Catherine" uniqKey="Lapierre C" first="Catherine" last="Lapierre">Catherine Lapierre</name><name sortKey="Le Bris, Philippe" sort="Le Bris, Philippe" uniqKey="Le Bris P" first="Philippe" last="Le Bris">Philippe Le Bris</name><name sortKey="Legee, Frederic" sort="Legee, Frederic" uniqKey="Legee F" first="Frédéric" last="Legée">Frédéric Legée</name><name sortKey="Roujol, David" sort="Roujol, David" uniqKey="Roujol D" first="David" last="Roujol">David Roujol</name><name sortKey="Soulhat, Camille" sort="Soulhat, Camille" uniqKey="Soulhat C" first="Camille" last="Soulhat">Camille Soulhat</name></country><country name="Allemagne"><region name="Brandebourg"><name sortKey="Proost, Sebastian" sort="Proost, Sebastian" uniqKey="Proost S" first="Sebastian" last="Proost">Sebastian Proost</name></region><name sortKey="Hansen, Bjoern Oest" sort="Hansen, Bjoern Oest" uniqKey="Hansen B" first="Bjoern Oest" last="Hansen">Bjoern Oest Hansen</name><name sortKey="Mutwil, Marek" sort="Mutwil, Marek" uniqKey="Mutwil M" first="Marek" last="Mutwil">Marek Mutwil</name><name sortKey="Vaid, Neha" sort="Vaid, Neha" uniqKey="Vaid N" first="Neha" last="Vaid">Neha Vaid</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Giorgi, Federico M" sort="Giorgi, Federico M" uniqKey="Giorgi F" first="Federico M" last="Giorgi">Federico M. Giorgi</name></noRegion></country><country name="Canada"><region name="Ontario"><name sortKey="Provart, Nicholas" sort="Provart, Nicholas" uniqKey="Provart N" first="Nicholas" last="Provart">Nicholas Provart</name></region><name sortKey="Pasha, Asher" sort="Pasha, Asher" uniqKey="Pasha A" first="Asher" last="Pasha">Asher Pasha</name></country><country name="Australie"><region name="Victoria (État)"><name sortKey="Persson, Staffan" sort="Persson, Staffan" uniqKey="Persson S" first="Staffan" last="Persson">Staffan Persson</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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