Authors: Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Hernández-Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto-Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, Georgios J. Pappas Jr, Soledad Saburido-Alvarez, Darek Kedra, Irene Gonzalez, Luca Cozzuto, Jessica Gómez-Garrido, María A. Aguilar-Morón, Nuria Andreu, O. Mario Aguilar, Jordi Garcia-Mas, Maik Zehnsdorf, Martín P. Vázquez, Alfonso Delgado-Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana P. Vianello-Brondani, José Luís García, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cedric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella & Roderic Guigó

Institutions: 

  • 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
  • Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
  • Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
  • New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
  • Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
  • Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
  • Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
  • Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
  • Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
  • IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
  • Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
  • Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
  • EMBRAPA Rice and Beans, Biotechnology Laboratory, Santo Antônio de Goiás, GO, 75375-000, Brazil
  • Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
  • Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
  • Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
  • Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain

Publication: Genome Biology

Date: February 2016

Full paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0883-6

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.