ALBERT

Description: Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Carretero-Paulet, Lorenzo -- Dereeper, Alexis -- Droc, Gaetan -- Guyot, Romain -- Pietrella, Marco -- Zheng, Chunfang -- Alberti, Adriana -- Anthony, Francois -- Aprea, Giuseppe -- Aury, Jean-Marc -- Bento, Pascal -- Bernard, Maria -- Bocs, Stephanie -- Campa, Claudine -- Cenci, Alberto -- Combes, Marie-Christine -- Crouzillat, Dominique -- Da Silva, Corinne -- Daddiego, Loretta -- De Bellis, Fabien -- Dussert, Stephane -- Garsmeur, Olivier -- Gayraud, Thomas -- Guignon, Valentin -- Jahn, Katharina -- Jamilloux, Veronique -- Joet, Thierry -- Labadie, Karine -- Lan, Tianying -- Leclercq, Julie -- Lepelley, Maud -- Leroy, Thierry -- Li, Lei-Ting -- Librado, Pablo -- Lopez, Loredana -- Munoz, Adriana -- Noel, Benjamin -- Pallavicini, Alberto -- Perrotta, Gaetano -- Poncet, Valerie -- Pot, David -- Priyono -- Rigoreau, Michel -- Rouard, Mathieu -- Rozas, Julio -- Tranchant-Dubreuil, Christine -- VanBuren, Robert -- Zhang, Qiong -- Andrade, Alan C -- Argout, Xavier -- Bertrand, Benoit -- de Kochko, Alexandre -- Graziosi, Giorgio -- Henry, Robert J -- Jayarama -- Ming, Ray -- Nagai, Chifumi -- Rounsley, Steve -- Sankoff, David -- Giuliano, Giovanni -- Albert, Victor A -- Wincker, Patrick -- Lashermes, Philippe -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. ; CIRAD, UMR Amelioration Genetique et Adaptation des Plantes Mediterraneennes et Tropicales (AGAP), F-34398 Montpellier, France. ; IRD, UMR Diversite Adaptation et Developpement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Nestle Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oe, BP 49716, 37097 Tours Cedex 2, France. ; ENEA Trisaia Research Center, 75026 Rotondella, Italy. ; Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France. ; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universitat Bielefeld, Universitatsstrasse 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultat, Universitat Bielefeld, 33594 Bielefeld, Germany. ; Institut National de la Recherche Agronomique (INRA), Unite de Recherches en Genomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China. ; Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Departament de Genetica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain. ; Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia. ; Laboratorio de Genetica Molecular, Nucleo de Biotecnologia (NTBio), Embrapa Recursos Geneticos e Biotecnologia, Final Av. W/5 Norte, Parque Estacao Biologia, Brasilia-DF 70770-917, Brazil. ; CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France. ; Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy. ; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia. ; Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India. ; Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA. ; BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA. ; Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Commissariat a l'Energie Atomique, Genoscope, Institut de Genomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Universite d'Evry, UMR 8030, CP5706, Evry, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr. ; Institut de Recherche pour le Developpement (IRD), UMR Resistance des Plantes aux Bioagresseurs (RPB) [Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. vaalbert@buffalo.edu pwincker@genoscope.cns.fr philippe.lashermes@ird.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25190796" target="_blank"〉PubMed〈/a〉

Description: Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Hont, Angelique -- Denoeud, France -- Aury, Jean-Marc -- Baurens, Franc-Christophe -- Carreel, Francoise -- Garsmeur, Olivier -- Noel, Benjamin -- Bocs, Stephanie -- Droc, Gaetan -- Rouard, Mathieu -- Da Silva, Corinne -- Jabbari, Kamel -- Cardi, Celine -- Poulain, Julie -- Souquet, Marlene -- Labadie, Karine -- Jourda, Cyril -- Lengelle, Juliette -- Rodier-Goud, Marguerite -- Alberti, Adriana -- Bernard, Maria -- Correa, Margot -- Ayyampalayam, Saravanaraj -- Mckain, Michael R -- Leebens-Mack, Jim -- Burgess, Diane -- Freeling, Mike -- Mbeguie-A-Mbeguie, Didier -- Chabannes, Matthieu -- Wicker, Thomas -- Panaud, Olivier -- Barbosa, Jose -- Hribova, Eva -- Heslop-Harrison, Pat -- Habas, Remy -- Rivallan, Ronan -- Francois, Philippe -- Poiron, Claire -- Kilian, Andrzej -- Burthia, Dheema -- Jenny, Christophe -- Bakry, Frederic -- Brown, Spencer -- Guignon, Valentin -- Kema, Gert -- Dita, Miguel -- Waalwijk, Cees -- Joseph, Steeve -- Dievart, Anne -- Jaillon, Olivier -- Leclercq, Julie -- Argout, Xavier -- Lyons, Eric -- Almeida, Ana -- Jeridi, Mouna -- Dolezel, Jaroslav -- Roux, Nicolas -- Risterucci, Ange-Marie -- Weissenbach, Jean -- Ruiz, Manuel -- Glaszmann, Jean-Christophe -- Quetier, Francis -- Yahiaoui, Nabila -- Wincker, Patrick -- England -- Nature. 2012 Aug 9;488(7410):213-7. doi: 10.1038/nature11241.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de cooperation Internationale en Recherche Agronomique pour le Developpement, UMR AGAP, F-34398 Montpellier, France. angelique.d'hont@cirad.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801500" target="_blank"〉PubMed〈/a〉

Description: Whole genome duplications (WGDs) occurred in the distant evolutionary history of many lineages and are particularly frequent in the flowering plant lineages. Following paleopolyploidization in plants, most duplicated genes are deleted by intrachromosomal recombination, a process referred to as fractionation. In the examples studied so far, genes are disproportionately lost from one of the parental subgenomes (biased fractionation) and the subgenome having lost the lowest number of genes is more expressed (genome dominance). In the present study, we analyzed the pattern of gene deletion and gene expression following the most recent WGD in banana (alpha event) and extended our analyses to seven other sequenced plant genomes: poplar, soybean, medicago, arabidopsis, sorghum, brassica, and maize. We propose a new class of ancient WGD, with Musa (alpha), poplar, and soybean as members, where genes are both deleted and expressed to an equal extent (unbiased fractionation and genome equivalence). We suggest that WGDs with genome dominance and biased fractionation (Class I) may result from ancient allotetraploidies, while WGDs without genome dominance or biased fractionation (Class II) may result from ancient autotetraploidies.

Description: : We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form Contact: valentin.guignon@cirad.fr ; stephanie.sidibe-bocs@cirad.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The whole genome sequence of Coffea canephora , the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub ( http://coffee-genome.org/ ), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.