title: Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.
abstract: BACKGROUND
  Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.
  
  
  RESULTS
  We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools.
  
  
  CONCLUSIONS
  The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Vlasova
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands.
authors.forename: Salvador
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authors.lastname: Capella-Gutiérrez
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
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authors.lastname: Rendón-Anaya
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
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authors.affiliation: Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia.
authors.forename: André E
authors.initials: AE
authors.lastname: Minoche
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Câmara
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Pablo
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authors.lastname: Prieto-Barja
authors.affiliation: New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.
authors.forename: André
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authors.affiliation: IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain.
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authors.affiliation: Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina.
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authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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authors.affiliation: Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil.
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authors.initials: GJ
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authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
authors.forename: Soledad
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authors.lastname: Saburido-Alvarez
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Darek
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authors.lastname: Kedra
authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
authors.forename: Irene
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authors.lastname: Gonzalez
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Luca
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authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Jessica
authors.initials: J
authors.lastname: Gómez-Garrido
authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
authors.forename: María A
authors.initials: MA
authors.lastname: Aguilar-Morón
authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
authors.forename: Nuria
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authors.affiliation: Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina.
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authors.affiliation: IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain.
authors.forename: Jordi
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authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
authors.forename: Maik
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authors.affiliation: Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina.
authors.forename: Martín P
authors.initials: MP
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authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
authors.forename: Alfonso
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authors.affiliation: Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico.
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authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
authors.forename: Ernesto
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authors.lastname: Lowy
authors.affiliation: Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina.
authors.forename: Alejandro
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authors.affiliation: Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain.
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authors.initials: JL
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authors.affiliation: Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.|CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Tyler
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authors.affiliation: Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
authors.forename: Federico
authors.initials: F
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authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
authors.forename: Heinz
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authors.affiliation: Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain.
authors.forename: Marta
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authors.lastname: Santalla
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Cedric
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authors.lastname: Notredame
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. toni.gabaldon@crg.eu.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. toni.gabaldon@crg.eu.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain. toni.gabaldon@crg.eu.
authors.forename: Toni
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authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico. aherrera@langebio.cinvestav.mx.
authors.forename: Alfredo
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authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. roderic.guigo@crg.eu.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain. roderic.guigo@crg.eu.|IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain. roderic.guigo@crg.eu.
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mesh_terms: D018744:DNA, Plant / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018745:Genome, Plant; D005838:Genotype; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D027805:Phaseolus / Q000235:genetics*; D010802:Phylogeny; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018744:DNA, Plant