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1. Overview of a surface-ripened cheese community functioning by meta-omics analyses.

Author

Eric Dugat-Bony, Cécile Straub, Aurélie Teissandier, Djamila Onésime, Valentin Loux, Christophe Monnet, Françoise Irlinger, Sophie Landaud, Marie-Noëlle Leclercq-Perlat, Pascal Bento, Sébastien Fraud, Jean-François Gibrat, Julie Aubert, Frédéric Fer, Eric Guédon, Nicolas Pons, Sean Kennedy, Jean-Marie Beckerich, Dominique Swennen, and Pascal Bonnarme

Subjects
Medicine, Science
Abstract

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.

Published
2015
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2. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Author

Jean-Charles Leplé, Céline Noirot, Antoine Kremer, Christian Burban, Hadi Quesneville, Michael Stierschneider, Valérie Léger, Saneyoshi Ueno, Pascal Bento, Corinne Da Silva, François Buscot, Silvia Fluch, Jérôme Bartholomé, Christophe Plomion, Christophe Klopp, Jean-Marc Aury, François Ehrenmann, Isabelle Lesur, Lasse Feldhahn, Joelle Amselem, Céline Lalanne, Florent Murat, Mika T. Tarkka, Jérôme Salse, Caroline Belser, Sylvie Herrmann, Grégoire Le Provost, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Biométrie et Intelligence Artificielle (UBIA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de Recherche Génomique Info (URGI), Austrian Institute of Technology [Vienna] (AIT), Department of Soil Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), German Centre for Integrative Biodiversity Research, Synthetic and Systems Biology Unit [Szeged], Biological Research Centre [Szeged] (BRC), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Biodiversité, Gènes et Communautés, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Helmholtz Centre for Environmental Research (UFZ), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Phénotype, Sequence assembly, UniGene, comparative genomics, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Gene Expression Regulation, Plant, bud phenology, K01 - Foresterie - Considérations générales, genomic features [EN], ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, biology, bourgeon, Chromosome Mapping, Plant Dormancy, Adaptation, Physiological, Quercus petraea, quercus, Quercus robur, Phénologie, Génotype, Genome, Plant, Research Article, Biotechnology, expression des gènes, Genome evolution, Genetic Speciation, education, fagaceae, de novo assembly, Séquence d'ARN, 03 medical and health sciences, oak, séquençage, Gene, 030304 developmental biology, transcriptome, RNA-seq, Comparative genomics, Base Sequence, Transcription génique, Sequence Analysis, RNA, génomique comparative, 15. Life on land, biology.organism_classification, dormance, Evolutionary biology, 010606 plant biology & botany
Abstract

Background Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1331-9) contains supplementary material, which is available to authorized users.

Published
2015
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3. Erratum for the Report: 'Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome' by B. Chalhoub, F. Denoeud, S. Liu, I. A. P. Parkin, H. Tang, X. Wang, J. Chiquet, H. Belcram, C. Tong, B. Samans, M. Corréa, C. Da Silva, J. Just, C. Falentin, C. S. Koh, I. Le Clainche, M. Bernard, P. Bento, B. Noel, K. Labadie, A. Alberti, M. Charles, D. Arnaud, H. Guo, C. Daviaud, S. Alamery, K. Jabbari, M. Zhao, P. P. Edger, H. Chelaifa, D. Tack, G. Lassalle, I. Mestiri, N. Schnel, M.-C. Le Paslier, G. Fan, V. Renault, P. E. Bayer, A. A. Golicz, S. Manoli, T.-H. Lee, V. Ha Dinh Thi, S. Chalabi, Q. Hu, C. Fan, R. Tollenaere, Y. Lu, C. Battail, J. Shen, C. H. D. Sidebottom, X. Wang, A. Canaguier, A. Chauveau, A. Bérard, G. Deniot, M. Guan, Z. Liu, F. Sun, Y. P. Lim, E. Lyons, C. D. Town, I. Bancroft, X. Wang, J. Meng, J. Ma, J. C. Pires, G. J. King, D. Brunel, R. Delourme, M. Renard, J.-M. Aury, K. L. Adams, J. Batley, R. J. Snowdon, J. Tost, D. Edwards, Y. Zhou, W. Hua, A. G. Sharpe, A. H. Paterson, C. Guan, P. Wincker

Author

Aurélie Canaguier, Christophe Battail, Jean-Marc Aury, Christopher D. Town, Christian Daviaud, David C. Tack, Wei Hua, Christine Sidebottom, Shengyi Liu, Reece Tollenaere, Sahana Manoli, Graham J.W. King, Fengming Sun, J. Shen, Victor Renault, Philipp E. Bayer, I. Le Clainche, Jacqueline Batley, Ian Bancroft, Nicolas Schnel, M. C. Le Paslier, Dominique Arnaud, Karine Labadie, Agnieszka A. Golicz, Dominique Brunel, Smahane Chalabi, Hui Guo, Yongming Zhou, Eric Lyons, Pascal Bento, Gilles Lassalle, Chunyun Guan, Yong Pyo Lim, Imen Mestiri, J. C. Pires, Guangyi Fan, Houda Chelaifa, Mei Guan, Tae-Ho Lee, Harry Belcram, Qiong Hu, F. Denoeud, Aurélie Chauveau, Andrew G. Sharpe, Bernard Noël, Boulos Chalhoub, Chaobo Tong, Adriana Alberti, Patrick Wincker, Jinling Meng, Birgit Samans, Patrick P. Edger, C. Da Silva, Margot Correa, Jianxin Ma, Régine Delourme, Keith L. Adams, Meixia Zhao, Haibao Tang, David Edwards, Andrew H. Paterson, Cyril Falentin, Zhongsong Liu, Julien Chiquet, Y. Lu, Xinfa Wang, Jérémy Just, V. Ha Dinh Thi, Kamel Jabbari, Chuchuan Fan, G. Deniot, Rod J. Snowdon, Jörg Tost, Aurélie Bérard, Mathieu Charles, Michel Renard, Salman Alamery, Maria Bernard, Isobel A. P. Parkin, and Chu Shin Koh

Subjects
Multidisciplinary, Botany, Brassica, Biology, biology.organism_classification, Genome
Published
2014
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4. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Author

Giorgio Graziosi, Maria Bernard, Michel Rigoreau, Adriana Muñoz, Olivier Garsmeur, Alan Carvalho Andrade, Qiong Zhang, Priyono, Xavier Argout, Lorenzo Carretero-Paulet, Thomas Gayraud, Giovanni Giuliano, Alexandre de Kochko, Steve Rounsley, Alberto Pallavicini, Benoît Bertrand, David Sankoff, Claudine Campa, Dominique Crouzillat, Patrick Wincker, Loretta Daddiego, François Anthony, Marie Christine Combes, Romain Guyot, Valentin Guignon, Katharina Jahn, Loredana Lopez, Pascal Bento, Stéphane Dussert, Christine Tranchant-Dubreuil, Maud Lepelley, Tianying Lan, Ray Ming, Thierry Joët, Gaëtan Droc, G. Aprea, Corinne Da Silva, Julio Rozas, David Pot, Véronique Jamilloux, Thierry Leroy, Benjamin Noel, Valérie Poncet, Pablo Librado, Adriana Alberti, Victor A. Albert, Jean-Marc Aury, Gaetano Perrotta, Philippe Lashermes, Robert VanBuren, Chunfang Zheng, Robert J Henry, Leiting Li, Julie Leclercq, Chifumi Nagai, Marco Pietrella, Karine Labadie, Jayarama, Stéphanie Bocs, Alberto Cenci, Fabien De Bellis, Mathieu Rouard, Alexis Dereeper, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Institut de Recherche pour le Développement (IRD), Résistance des plantes aux bio-agresseurs (UMR RPB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Agenzia Nazionale per le nuove Tecnologie, l’energia e lo sviluppo economico sostenibile = Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Department of Mathematics and Statistics [Ottawa], University of Ottawa [Ottawa], Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bioversity, Parc Scientifique Agropolis II, Nestlé France, Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Chongqing University of Science & Technology, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Universitat de Barcelona (UB), Department of Mathematics [College Park], University of Maryland [College Park], University of Maryland System-University of Maryland System, Università degli studi di Trieste = University of Trieste, Indonesian Coffee and Cocoa Research Institute, Partenaires INRAE, Embrapa Recursos Genéticos e Biotecnologia [Brasília], Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Hawaii Agriculture Research Center, University of Arizona, Australian Research Council, Natural Sciences and Engineering Research Council of Canada, CNR-ENEA Agrifood Project A2 C44 L191, FINEP-Qualicafe, NSF 0922742 0922545, College of Arts and Sciences, University at Buffalo, SouthGreen Bioinformatics platform (UMR AGAP), CIRAD, INCT-CAFE, ANR-08-GENM-022-001, ANR-09-GENM-014-002, ANR-08-GENM-0022,GénomeCafé,Analyses de séquences d'extrémités de clones BAC comme étape préliminaire au séquençage du génome des caféiers(2008), ANR-09-GENM-0014,COFFEASEQ,Séquençage du génome du caféier (Coffea canephora)(2009), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Montpellier 2 - Sciences et Techniques (UM2)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Department of Mathematics, University of Maryland, University of Trieste, Giuliano, G., Perrotta, G., Lopez, Daddiego, L., Aprea, G., Pietrella, M., Denoeud, France, Carretero Paulet, Lorenzo, Dereeper, Alexi, Droc, Gaëtan, Guyot, Romain, Pietrella, Marco, Zheng, Chunfang, Alberti, Adriana, Anthony, Françoi, Aprea, Giuseppe, Aury, Jean Marc, Bento, Pascal, Bernard, Maria, Bocs, Stéphanie, Campa, Claudine, Cenci, Alberto, Combes, Marie Christine, Crouzillat, Dominique, Da Silva, Corinne, Daddiego, Loretta, De Bellis, Fabien, Dussert, Stéphane, Garsmeur, Olivier, Gayraud, Thoma, Guignon, Valentin, Jahn, Katharina, Jamilloux, Véronique, Joët, Thierry, Labadie, Karine, Lan, Tianying, Leclercq, Julie, Lepelley, Maud, Leroy, Thierry, Li, Lei Ting, Librado, Pablo, Lopez, Loredana, Muñoz, Adriana, Noel, Benjamin, Pallavicini, Alberto, Perrotta, Gaetano, Poncet, Valérie, Pot, David, Priyono, P., Rigoreau, Michel, Rouard, Mathieu, Rozas, Julio, Tranchant Dubreuil, Christine, Vanburen, Robert, Zhang, Qiong, Andrade, Alan C., Argout, Xavier, Bertrand, Benoît, De Kochko, Alexandre, Graziosi, Giorgio, Henry, Robert J., Jayarama, J., Ming, Ray, Nagai, Chifumi, Rounsley, Steve, Sankoff, David, Giuliano, Giovanni, Albert, Victor A., Wincker, Patrick, and Lashermes, Philippe

Subjects
Phylogénie, [SDV]Life Sciences [q-bio], Coffea, Évolution, biosynthèse, Genome, Camellia sinensis, F30 - Génétique et amélioration des plantes, chemistry.chemical_compound, Solanum lycopersicum, genetics, Methyltransferase, Phylogeny, Plant Proteins, caffeine, 2. Zero hunger, Genetics, Multidisciplinary, Medicine (all), Plant Protein, food and beverages, F70 - Taxonomie végétale et phytogéographie, Caféine, Caffeine, Genome, Plant, coffea, Canephora, F60 - Physiologie et biochimie végétale, Biology, Transférase, Coffea canephora, Evolution, Molecular, Phylogenetics, evolution, Methyltransferases, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Theobroma cacao, Gene, genome, Génome, Molecular, Plant, biology.organism_classification, chemistry, Angiosperme
Abstract

Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution. Science , this issue p. 1181 ; see also p. 1124

Published
2014
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5. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Author

Boulos, Chalhoub, France, Denoeud, Shengyi, Liu, Isobel A P, Parkin, Haibao, Tang, Xiyin, Wang, Julien, Chiquet, Harry, Belcram, Chaobo, Tong, Birgit, Samans, Margot, Corréa, Corinne, Da Silva, Jérémy, Just, Cyril, Falentin, Chu Shin, Koh, Isabelle, Le Clainche, Maria, Bernard, Pascal, Bento, Benjamin, Noel, Karine, Labadie, Adriana, Alberti, Mathieu, Charles, Dominique, Arnaud, Hui, Guo, Christian, Daviaud, Salman, Alamery, Kamel, Jabbari, Meixia, Zhao, Patrick P, Edger, Houda, Chelaifa, David, Tack, Gilles, Lassalle, Imen, Mestiri, Nicolas, Schnel, Marie-Christine, Le Paslier, Guangyi, Fan, Victor, Renault, Philippe E, Bayer, Agnieszka A, Golicz, Sahana, Manoli, Tae-Ho, Lee, Vinh Ha Dinh, Thi, Smahane, Chalabi, Qiong, Hu, Chuchuan, Fan, Reece, Tollenaere, Yunhai, Lu, Christophe, Battail, Jinxiong, Shen, Christine H D, Sidebottom, Xinfa, Wang, Aurélie, Canaguier, Aurélie, Chauveau, Aurélie, Bérard, Gwenaëlle, Deniot, Mei, Guan, Zhongsong, Liu, Fengming, Sun, Yong Pyo, Lim, Eric, Lyons, Christopher D, Town, Ian, Bancroft, Xiaowu, Wang, Jinling, Meng, Jianxin, Ma, J Chris, Pires, Graham J, King, Dominique, Brunel, Régine, Delourme, Michel, Renard, Jean-Marc, Aury, Keith L, Adams, Jacqueline, Batley, Rod J, Snowdon, Jorg, Tost, David, Edwards, Yongming, Zhou, Wei, Hua, Andrew G, Sharpe, Andrew H, Paterson, Chunyun, Guan, and Patrick, Wincker

Subjects
Evolution, Molecular, Polyploidy, Brassica napus, Chromosome Duplication, Seeds, Genome, Plant
Abstract

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Published
2014

6. Early allopolyploid evolution in the post-Neolithic[i] Brassica napus[/i] oilseed genome

Author

Patrick Wincker, Pascal Bento, Sahana Manoli, Agnieszka A. Golicz, G. Deniot, Shengyi Liu, Christine Sidebottom, Chu Shin Koh, Ian Bancroft, Christian Daviaud, David C. Tack, Rod J. Snowdon, Jörg Tost, Guangyi Fan, Hui Guo, Smahane Chalabi, Boulos Chalhoub, Xinfa Wang, Harry Belcram, Aurélie Chauveau, Gilles Lassalle, Jean-Marc Aury, Tae-Ho Lee, Houda Chelaifa, Jinling Meng, Christopher D. Town, Haibao Tang, Zhongsong Liu, Julien Chiquet, Andrew G. Sharpe, Salman Alamery, Chunyun Guan, Mathieu Charles, Qiong Hu, Xiyin Wang, Xiaowu Wang, Jianxin Ma, Régine Delourme, Mei Guan, Eric Lyons, Chaobo Tong, Margot Correa, Adriana Alberti, Keith L. Adams, Patrick P. Edger, Marie-Christine Le Paslier, Yunhai Lu, Corinne Da Silva, Christophe Battail, Andrew H. Paterson, Isabelle Le Clainche, Benjamin Noel, Jérémy Just, Jacqueline Batley, Jinxiong Shen, Fengming Sun, Kamel Jabbari, Karine Labadie, Michel Renard, Maria Bernard, Birgit Samans, Aurélie Canaguier, Isobel A. P. Parkin, Yong Pyo Lim, Vinh Ha Dinh Thi, Victor Renault, Meixia Zhao, David Edwards, Graham J.W. King, Nicolas Schnel, Dominique Brunel, Cyril Falentin, Reece Tollenaere, Aurélie Bérard, Yongming Zhou, Dominique Arnaud, Imen Mestiri, Philippe E. Bayer, Chuchuan Fan, Wei Hua, J. Chris Pires, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Oil Crops Research Institute, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture-Chinese Academy of Agricultural Sciences (CAAS), Agriculture and Agri-Food (AAFC), J. Craig Venter Institute [La Jolla, USA] (JCVI), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University (FAFU), University of Georgia [USA], School of Life Sciences, Center of Genomics and Computational Biology, Hebei United University, Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Research Center for Biosystems, Land Use and Nutrition, Department of Plant Breeding, Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, National Research Council of Canada (NRC), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Centre National de Genotypage, Plant Genome Mapping Laboratory, Laboratoire épigénétique et environnement, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Cologne Center for Genomics, University of Cologne, Department of Agronomy, Purdue University [West Lafayette], Department of Plant and Microbial Biology, University of California (UC), Department of Botany [Vancouver] (UBC Botany), University of British Columbia (UBC), National Key Laboratory of Crop Genetic Improvement [China], Huazhong Agricultural University [Wuhan] (HZAU), Beijing Genome Institute, Fondation Jean Dausset - Centre d’Étude du Polymorphisme Humain, College of Agronomy, Hunan Agricultural University [Changsha], Department of Horticulture, Molecular Genetics and Genomics Laboratory, Chungnam National University (CNU), School of Plant Sciences, iPlant Collaborative, University of Arizona, Department of Biology, University of York [York, UK], Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Division of Biological Sciences, University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Southern Cross Plant Science, Southern Cross University (SCU), School of Plant Biology, The University of Western Australia (UWA), Laboratory for Epigenetics and Environment, Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire de Mathématiques et Modélisation d'Evry, Justus-Liebig-Universität Gießen (JLU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of California, Huazhong Agricultural University, Euralis Semences, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), BIOGEMMA, Unité de Recherches Zootechniques (URZ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Limagrain, J. Craig Venter Institute, Fujian Agriculture and Forestry University, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Botany, University of Missouri [Columbia], Southern Cross University, Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1165 Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique ( INRA ) -Université d'Evry Val d'Essonne, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ministry of Agriculture-Chinese Academy of Agricultural Sciences ( CAAS ), Agriculture and Agri-Food [Ottawa] ( AAFC ), University of Georgia, Laboratoire de Mathématiques et Modélisation d'Evry ( LaMME ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -ENSIIE-Centre National de la Recherche Scientifique ( CNRS ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Justus Liebig University Giessen, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, National Research Council of Canada ( NRC ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut National de la Recherche Agronomique ( INRA ), University of British Columbia ( UBC ), National Key Laboratory of Crop Genetic Improvement, Chungnam National University, Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), University of Missouri ( Saisissez le sigle en majuscules sans points ), The University of Western Australia ( UWA ), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, plant genome, [SDV]Life Sciences [q-bio], Brassica, rapeseed, Biology, 01 natural sciences, Genome, Evolution, Molecular, Polyploidy, 03 medical and health sciences, chemistry.chemical_compound, Gene duplication, genetics, Epigenetics, Domestication, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], molecular evolution, Brassica napus, chromosome duplication, food and beverages, plant seed, biology.organism_classification, chemistry, Glucosinolate, Seeds, cytology, Genome, Plant, 010606 plant biology & botany
Abstract

Oilseed rape (Brassica napus L.) was formed ∼7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content.We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement., Erratum published in Vol 345, no. 6202 September 2014 DOI: 10.1126/science.1260782

Published
2014
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7. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Author

Patrick Wincker, Pascal Bento, Benjamin Noel, Cédric Cabau, Jean-Marc Aury, Yann Guiguen, Alexandra Louis, Edwige Quillet, Carine Genet, Julien Bobe, Maria Bernard, Mekki Boussaha, Camille Berthelot, Olivier Jaillon, Delphine Galiana, Jean-Nicolas Volff, Christophe Klopp, Domitille Chalopin, Corinne Da Silva, Patrice Dehais, Christine Gaspin, Karine Labadie, Frédéric Brunet, Gary H. Thorgaard, Adriana Alberti, Philippe Bardou, Jérôme Montfort, Amélie Juanchich, Hugues Roest Crollius, René Guyomard, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Welcome Trust Genome Campus, Hinxton, European Bioinformatics Institute, École normale supérieure - Lyon (ENS Lyon), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), School of Biological Sciences, Washington State University (WSU), Université d'Évry-Val-d'Essonne (UEVE), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR (Genotrout project, ANR-09-GENM-001) Génomique et Biotechnologies Végétales, Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], ProdInra, Archive Ouverte, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
phylogénétique, [SDV]Life Sciences [q-bio], séquençage du génome complet, General Physics and Astronomy, Whole genome duplication, Vertebrate genome, Biology, Gene Deletions, Genome, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, poisson, Gene Duplication, biology.animal, phylogénie, Animals, analyse génomique, duplication des génomes, Gene, salmonidae, Genetics, oncorhynchus mykiss, Multidisciplinary, génome, évolution animale, Vertebrate, General Chemistry, biology.organism_classification, Spotted gar, [SDV] Life Sciences [q-bio], évolution des espèces, Vertebrates, Rainbow trout, analyse génétique, truite arc en ciel, expression des gènes
Abstract

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions., Although whole-genome duplications (WGDs) are rare events, they have an important role in shaping vertebrate evolution. Here, the authors sequence the rainbow trout genome and show that rediploidization after WGD occurs in a slow and stepwise manner.

Published
2014
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8. Genome Sequence of Corynebacterium casei UCMA 3821, Isolated from a Smear-Ripened Cheese

Author

Françoise Irlinger, Valentin Loux, Jean-François Gibrat, Christophe Monnet, Pascal Bonnarme, Pascal Bento, Cécile Straub, Sophie Landaud, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mathématique, Informatique et Génome (MIG), and Institut National de la Recherche Agronomique (INRA)

Subjects
Surface, Annotation, Molecular Sequence Data, Biology, Corynebacterium, Microbiology, Database, 03 medical and health sciences, Cheese, Corynebacterium casei, bioinformatique, Molecular Biology, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, STRUCTURE DU GENOME, Base Sequence, 030306 microbiology, Microbiology and Parasitology, Flore, Microbiologie et Parasitologie, Genome Announcements, RNA Genes, Biodiversité, Microflore, soft, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genome, Bacterial
Abstract

Corynebacterium casei is one of the most prevalent species present on the surfaces of smear-ripened cheeses, where it contributes to the production of the desired organoleptic properties. Here, we report the draft genome sequence of Corynebacterium casei UCMA 3821 to provide insights into its physiology.

Published
2012
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9. Genome sequence of Staphylococcus equorum subsp equorum Mu2, Isolated from a french smear-ripened cheese

Author

Cécile Straub, Jean-François Gibrat, Françoise Irlinger, Christophe Monnet, Valentin Loux, Pascal Bonnarme, Sophie Landaud, Pascal Bento, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mathématique, Informatique et Génome (MIG), and Institut National de la Recherche Agronomique (INRA)

Subjects
DNA, Bacterial, coagulase-negative staphylococci, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, fermented sausages, RNA genes, Molecular Sequence Data, medicine.disease_cause, Microbiology, 03 medical and health sciences, Cheese, medicine, Staphylococcus species, Molecular Biology, Fermentation in food processing, Aroma, 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, génome, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Staphylococcus equorum, Genome Announcements, staphylococcus, Staphylococcus, Genome, Bacterial
Abstract

Staphylococcus equorumsubsp.equorumis a member of the coagulase-negative staphylococcus group and is frequently isolated from fermented food products and from food-processing environments. It contributes to the formation of aroma compounds during the ripening of fermented foods, especially cheeses and sausages. Here, we report the draft genome sequence ofStaphylococcus equorumsubsp.equorumMu2 to provide insights into its physiology and compare it with otherStaphylococcusspecies.

Published
2012
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10. Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

Author

Sophie Landaud, Sébastien Fraud, Cécile Straub, Julie Aubert, Djamila Onesime, Eric Dugat-Bony, Jean-François Gibrat, Françoise Irlinger, Nicolas Pons, Dominique Swennen, Aurélie Teissandier, Christophe Monnet, Eric Guédon, Sean Kennedy, Jean-Marie Beckerich, Valentin Loux, Pascal Bento, M.-N. Leclercq-Perlat, Pascal Bonnarme, Frédéric Fer, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), ACTALIA [Villers-Bocage], MetaGenoPolis, This work was supported by the ExEco program (a joint metatranscriptomic and biochemical approach to the cheese ecosystem: for an improved monitoring of the expression of a complex food ecosystem) (ANR-09-ALIA-012-01), funded by the French National Research Agency (ANR)., We thank Serge Casaregola and Guillaume Morel (INRA, UMR1319 Micalis, Thiverval-Grignon, France) for providing the genome of G. candidum ATCC 204307, and Anne Sophie Sarthou and Jessie Castellote (INRA, UMR782 GMPA, Thiverval-Grignon, France) for technical assistance. We are grateful to our undergraduate bioinformatics students Maxime Ferrier, Roxane Boyer and Joeffrey Boggio (IUT Génie Biologique option bioinfomatique, Aurillac, France) for the development of scripts for functional classification, and Nicolas Parisot (Université d’Auvergne, Clermont-Ferrand, France) for supervising their work., ANR-09-ALIA-0012,EXECO,Etude méta-transcriptomique et biochimique de l?écosystème fromager : pour un contrôle accru de l?EXpression d?un ECOsystème alimentaire complexe.(2009), US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), ExEco program - French National Research Agency (ANR) ANR-09-ALIA-012-01, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
MESH: Cheese, Differential expression analysis, penicillium-camemberti, [SDV]Life Sciences [q-bio], lcsh:Medicine, Biochemical Process, Cheese ripening, Computational biology, Community functioning, Cheese, metabolic-activity, Maturation process, transcription-quantitative pcr, lcsh:Science, ComputingMilieux_MISCELLANEOUS, lactic-acid bacteria, 2. Zero hunger, emmentaler cheese, Multidisciplinary, biology, business.industry, Microbiota, metagenomic analysis, MESH: Transcriptome, lcsh:R, food and beverages, biology.organism_classification, gene-expression, MESH: Microbiota, Biotechnology, Microbial population biology, Metagenomics, Penicillium camemberti, debaryomyces-hansenii, saccharomyces-cerevisiae, geotrichum-candidum, lcsh:Q, MESH: Metagenomics, Transcriptome, business, Research Article
Abstract

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.

Published
2015
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