Adaptive gene loss in the common bean pan-genome during range expansion and domestication
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. Food legumes provide valuable resources to address global challenges such as climate change, biodiversity conservation, and the need for sustainable agriculture and healthy diets 1-3 . The common bean (Phaseolus vulgaris L.) is a diploid (2n = 2x = 22) and predominantly self-pollinating annual grain legume crop with a prominent role in agriculture and society 4-6 . It is also an ideal evolutionary model to study adaptive diversity in wild and domesticated legume populations 7 . The use of P. vulgaris as an evolutionary model reflects the parallel and independent life history of two geographically isolated, genetically differentiated gene pools (Mesoamerican and Andean) following its wild expansion from Mexico to South America ~150,000-200,000 years ago, long before its dual domestication 8-11 . Previous studies using a single reference genome have provided insights into the population structure of the common bean 12 and the genetic basis of important adaptive traits 13 . However, pan-genomic diversity must be explored in detail to gain a more comprehensive understanding 14-17 .Here, we describe the construction of a P. vulgaris pan-genome using a non-iterative approach and an analysis of its genetic diversity in terms of presence/absence variants (PAVs) within a representative panel of genetically and phenotypically well-characterized accessions. This publicly available common bean pan-genome will provide a valuable starting point to identify genes and genomic mechanisms
Domaines
Sciences du Vivant [q-bio]| Origine | Fichiers produits par l'(les) auteur(s) |
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