title: Genomic history of the origin and domestication of common bean unveils its closest sister species.
abstract: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.
  
  
  
  We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.
  
  
  
  We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
authors.forename: Martha
authors.initials: M
authors.lastname: Rendón-Anaya
authors.affiliation: Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico.
authors.forename: Josaphat M
authors.initials: JM
authors.lastname: Montero-Vargas
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
authors.forename: Soledad
authors.initials: S
authors.lastname: Saburido-Álvarez
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 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: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutierrez
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
authors.forename: José Juan
authors.initials: JJ
authors.lastname: Ordaz-Ortiz
authors.affiliation: Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina.
authors.forename: O Mario
authors.initials: OM
authors.lastname: Aguilar
authors.affiliation: EMBRAPA Rice and Beans, Biotechnology Laboratory, Santo Antônio de Goiás, GO, 75375-000, Brazil.
authors.forename: Rosana P
authors.initials: RP
authors.lastname: Vianello-Brondani
authors.affiliation: Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Santalla
authors.affiliation: Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, Irapuato, Guanajuato, Mexico.
authors.forename: Luis
authors.initials: L
authors.lastname: Delaye
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616-8780, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Gepts
authors.affiliation: Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico.
authors.forename: Robert
authors.initials: R
authors.lastname: Winkler
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Delgado-Salinas
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico. alfredo.herrera@cinvestav.mx.
authors.forename: Alfredo
authors.identifier: 0000-0002-4589-6870
authors.initials: A
authors.lastname: Herrera-Estrella
mesh_terms: D000071278:Domestication; D005419:Flavonoids / Q000096:biosynthesis; D051456:Gene Flow; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D027805:Phaseolus / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D018521:Plant Physiological Phenomena / Q000235:genetics; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D005419:Flavonoids
keywords: Adaptive traits; Common bean; Domestication; Genomic introgression; Speciation