Nature Communications (Aug 2024)
Adaptive gene loss in the common bean pan-genome during range expansion and domestication
- Gaia Cortinovis,
- Leonardo Vincenzi,
- Robyn Anderson,
- Giovanni Marturano,
- Jacob Ian Marsh,
- Philipp Emanuel Bayer,
- Lorenzo Rocchetti,
- Giulia Frascarelli,
- Giovanna Lanzavecchia,
- Alice Pieri,
- Andrea Benazzo,
- Elisa Bellucci,
- Valerio Di Vittori,
- Laura Nanni,
- Juan José Ferreira Fernández,
- Marzia Rossato,
- Orlando Mario Aguilar,
- Peter Laurent Morrell,
- Monica Rodriguez,
- Tania Gioia,
- Kerstin Neumann,
- Juan Camilo Alvarez Diaz,
- Ariane Gratias,
- Christophe Klopp,
- Elena Bitocchi,
- Valérie Geffroy,
- Massimo Delledonne,
- David Edwards,
- Roberto Papa
Affiliations
- Gaia Cortinovis
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Leonardo Vincenzi
- Department of Biotechnology, University of Verona
- Robyn Anderson
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia
- Giovanni Marturano
- Department of Biotechnology, University of Verona
- Jacob Ian Marsh
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia
- Philipp Emanuel Bayer
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia
- Lorenzo Rocchetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Giovanna Lanzavecchia
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Alice Pieri
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara
- Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Juan José Ferreira Fernández
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19
- Marzia Rossato
- Department of Biotechnology, University of Verona
- Orlando Mario Aguilar
- Institute of Biotechnology and Molecular Biology, UNLP-CONICET, CCT La Plata
- Peter Laurent Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota
- Monica Rodriguez
- Department of Agriculture, University of Sassari
- Tania Gioia
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata
- Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
- Juan Camilo Alvarez Diaz
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay
- Ariane Gratias
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay
- Christophe Klopp
- INRAE, Genotoul Bioinformatics Platform, Applied Mathematics and Informatics of Toulouse, Sigenae, MIAT
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- Valérie Geffroy
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay
- Massimo Delledonne
- Department of Biotechnology, University of Verona
- David Edwards
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia
- Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University
- DOI
- https://doi.org/10.1038/s41467-024-51032-2
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 15
Abstract
Abstract The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
