Phylogenomics: The Evolution of Common Bean as Seen from the Perspective of All of Its Genes

  • Salvador Capella-GutiérrezEmail author
  • Anna Vlasova
  • Toni GabaldónEmail author
Part of the Compendium of Plant Genomes book series (CPG)


Phaseolus vulgaris is the most important legume species for human nourishment. However, until very recently genomics resources for this plant have been scarce, which preventing fully understanding the parallel domestications occurred at two geographical regions: Mesoamerica and Andes. The first reference genome for P. vulgaris, the Andean landrace G19833, was published in 2014, followed in 2016 by the Mesoamerican reference genome, the breeding line BAT93. These resources have allowed elucidating the evolutionary trajectory of P. vulgaris as species, and of both gene pools. First, it has been possible to confirm that the common bean has not undergone a specific whole genome duplication event similarly to the one of Glycine max around ~12 million years ago. Second, there is a high degree of concordance between both gene pools in terms of gene content and evolutionary profiles. This includes also the pattern of specialization of gene expression profiles across different relative evolutionary ages. We confirmed the trend observed for the Mesoamerican genome: retained duplicated genes tend to specialize their expression profiles overtime. New analyses using available transcriptomic data gene co-expression networks for both gene pools have been generated and compared for this review in order to look for commonalities and differences. Genes associated to photosynthesis and to response to different stresses account for the largest modules of these networks, although some differences were detected which may have roles in the domestication syndrome of both gene pools. However, more sequencing data are needed to a better understanding of common bean genome function and to deepen on the domestication processes of both gene pools. It is expected that third generation sequencing technologies will play an important role in those efforts, leading to better genome assemblies and gene-sets. This will focus further efforts on improving breeding lines while keeping genetic diversity of landraces and wild accessions of P. vulgaris.


Common bean BAT93 G19833 Legumes Gene duplication Phylogenomics Transcriptome 


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© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)BarcelonaSpain
  2. 2.Universitat Pompeu Fabra (UPF)BarcelonaSpain
  3. 3.Spanish National Bioinformatics Institute (INB)Spanish National Cancer Research Centre (CNIO)MadridSpain
  4. 4.Institució Catalana de Recerca I Estudis Avançats (ICREA)BarcelonaSpain

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