@article {209,
	title = {The banana genome hub.},
	journal = {Database : the journal of biological databases and curation},
	volume = {2013},
	year = {2013},
	month = {2013},
	pages = {bat035},
	abstract = {Banana is one of the world{\textquoteright}s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/},
	issn = {1758-0463},
	doi = {10.1093/database/bat035},
	author = {Ga{\"e}tan Droc and Larivi{\`e}re, Delphine and Valentin Guignon and Yahiaoui, Nabila and This, Dominique and Olivier Garsmeur and Dereeper, Alexis and Hamelin, Chantal and Argout, Xavier and Dufayard, Jean-Fran{\c c}ois and Lengelle, Juliette and Franc-Christophe Baurens and Cenci, Alberto and Pitollat, Bertrand and D{\textquoteright}Hont, Ang{\'e}lique and Ruiz, Manuel and Mathieu Rouard and Bocs, St{\'e}phanie}
}
@article {198,
	title = {The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.},
	journal = {Nature},
	volume = {488},
	year = {2012},
	month = {2012 Aug 9},
	pages = {213-7},
	abstract = {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.},
	keywords = {Conserved Sequence, DNA Transposable Elements, Evolution, Molecular, Gene Duplication, Genes, Plant, Genome, Plant, Genotype, Haploidy, Molecular Sequence Data, Musa, Phylogeny},
	issn = {1476-4687},
	doi = {10.1038/nature11241},
	author = {D{\textquoteright}Hont, Ang{\'e}lique and Denoeud, France and Aury, Jean-Marc and Franc-Christophe Baurens and Carreel, Fran{\c c}oise and Olivier Garsmeur and Noel, Benjamin and Bocs, St{\'e}phanie and Ga{\"e}tan Droc and Mathieu Rouard and Da Silva, Corinne and Jabbari, Kamel and Cardi, C{\'e}line and Poulain, Julie and Souquet, Marl{\`e}ne and Labadie, Karine and Jourda, Cyril and Lengell{\'e}, Juliette and Rodier-Goud, Marguerite and Alberti, Adriana and Bernard, Maria and Correa, Margot and Ayyampalayam, Saravanaraj and Mckain, Michael R and Leebens-Mack, Jim and Burgess, Diane and Freeling, Mike and Mb{\'e}gui{\'e}-A-Mb{\'e}gui{\'e}, Didier and Chabannes, Matthieu and Wicker, Thomas and Panaud, Olivier and Barbosa, Jose and Hribova, Eva and Heslop-Harrison, Pat and Habas, R{\'e}my and Rivallan, Ronan and Francois, Philippe and Claire Poiron and Kilian, Andrzej and Burthia, Dheema and Jenny, Christophe and Bakry, Fr{\'e}d{\'e}ric and Brown, Spencer and Valentin Guignon and Kema, Gert and Dita, Miguel and Waalwijk, Cees and Joseph, Steeve and Dievart, Anne and Jaillon, Olivier and Leclercq, Julie and Argout, Xavier and Lyons, Eric and Almeida, Ana and Jeridi, Mouna and Dolezel, Jaroslav and Roux, Nicolas and Risterucci, Ange-Marie and Weissenbach, Jean and Ruiz, Manuel and Glaszmann, Jean-Christophe and Qu{\'e}tier, Francis and Yahiaoui, Nabila and Wincker, Patrick}
}
@article {199,
	title = {The genome of Theobroma cacao.},
	journal = {Nature genetics},
	volume = {43},
	year = {2011},
	month = {2011 Feb},
	pages = {101-8},
	abstract = {We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76\% of the estimated genome size and contains almost all previously described genes, with 82\% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.},
	keywords = {Cacao, Cell Nucleus, DNA, DNA Transposable Elements, Evolution, Molecular, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Genotype, Homozygote, In Situ Hybridization, Models, Genetic, Quantitative Trait Loci},
	issn = {1546-1718},
	doi = {10.1038/ng.736},
	author = {Argout, Xavier and Salse, Jerome and Aury, Jean-Marc and Guiltinan, Mark J and Droc, Gaetan and Gouzy, Jerome and Allegre, Mathilde and Chaparro, Cristian and Legavre, Thierry and Maximova, Siela N and Abrouk, Michael and Murat, Florent and Fouet, Olivier and Poulain, Julie and Ruiz, Manuel and Roguet, Yolande and Rodier-Goud, Maguy and Barbosa-Neto, Jose Fernandes and Sabot, Francois and Kudrna, Dave and Ammiraju, Jetty Siva S and Schuster, Stephan C and Carlson, John E and Sallet, Erika and Schiex, Thomas and Dievart, Anne and Kramer, Melissa and Gelley, Laura and Shi, Zi and B{\'e}rard, Aur{\'e}lie and Viot, Christopher and Boccara, Michel and Risterucci, Ange Marie and Valentin Guignon and Sabau, Xavier and Axtell, Michael J and Ma, Zhaorong and Zhang, Yufan and Brown, Spencer and Bourge, Mickael and Golser, Wolfgang and Song, Xiang and Clement, Didier and Rivallan, Ronan and Tahi, Mathias and Akaza, Joseph Moroh and Pitollat, Bertrand and Gramacho, Karina and D{\textquoteright}Hont, Ang{\'e}lique and Brunel, Dominique and Infante, Diogenes and Kebe, Ismael and Costet, Pierre and Wing, Rod and McCombie, W Richard and Guiderdoni, Emmanuel and Quetier, Francis and Panaud, Olivier and Wincker, Patrick and Bocs, Stephanie and Lanaud, Claire}
}
