Adaptive gene loss in the common bean pan-genome during range expansion and domestication.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
07 Aug 2024
Historique:
received: 15 12 2023
accepted: 28 07 2024
medline: 7 8 2024
pubmed: 7 8 2024
entrez: 6 8 2024
Statut: epublish

Résumé

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.

Identifiants

pubmed: 39107305
doi: 10.1038/s41467-024-51032-2
pii: 10.1038/s41467-024-51032-2
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

6698

Subventions

Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 862862

Informations de copyright

© 2024. The Author(s).

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Auteurs

Gaia Cortinovis (G)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Leonardo Vincenzi (L)

Department of Biotechnology, University of Verona, 37134, Verona, Italy.

Robyn Anderson (R)

Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.

Giovanni Marturano (G)

Department of Biotechnology, University of Verona, 37134, Verona, Italy.

Jacob Ian Marsh (JI)

Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.

Philipp Emanuel Bayer (PE)

Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.

Lorenzo Rocchetti (L)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Giulia Frascarelli (G)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Giovanna Lanzavecchia (G)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Alice Pieri (A)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Andrea Benazzo (A)

Department of Life Sciences and Biotechnology, University of Ferrara, 44100, Ferrara, Italy.

Elisa Bellucci (E)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Valerio Di Vittori (V)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Laura Nanni (L)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Juan José Ferreira Fernández (JJ)

Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Asturias, Spain.

Marzia Rossato (M)

Department of Biotechnology, University of Verona, 37134, Verona, Italy.
Genartis s.r.l, 37126, Verona, Italy.

Orlando Mario Aguilar (OM)

Institute of Biotechnology and Molecular Biology, UNLP-CONICET, CCT La Plata, La Plata, Argentina.

Peter Laurent Morrell (PL)

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108-6026, USA.

Monica Rodriguez (M)

Department of Agriculture, University of Sassari, 07100, Sassari, Italy.
CBV-Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, University of Sassari, 07041, Alghero, Italy.

Tania Gioia (T)

School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100, Potenza, Italy.

Kerstin Neumann (K)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Germany.

Juan Camilo Alvarez Diaz (JC)

CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France.

Ariane Gratias (A)

CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France.

Christophe Klopp (C)

INRAE, Genotoul Bioinformatics Platform, Applied Mathematics and Informatics of Toulouse, Sigenae, MIAT, UR875, Castanet Tolosan, France.

Elena Bitocchi (E)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.

Valérie Geffroy (V)

CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), University of Evry, University Paris-Saclay, 91405, Orsay, France.

Massimo Delledonne (M)

Department of Biotechnology, University of Verona, 37134, Verona, Italy.
Genartis s.r.l, 37126, Verona, Italy.

David Edwards (D)

Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.

Roberto Papa (R)

Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy. r.papa@univpm.it.

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