Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131, Ancona, Italy.
Department of Biotechnology, University of Verona, 37134, Verona, Italy.
Nat Commun. 2024 Aug 7;15(1):6698. doi: 10.1038/s41467-024-51032-2.
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.
普通菜豆（Phaseolus vulgaris L.）是一种重要的豆科作物，也是研究野生和驯化群体适应性多样性的理想进化模型。在这里，我们基于五个高质量基因组和代表 339 个基因型的全基因组读数，展示了普通菜豆的泛基因组。它揭示了约 234 Mb 的额外序列，其中包含参考基因组中缺失的 6905 个蛋白质编码基因，构成所有存在/缺失变异（PAV）的 49%。PAV 中的非同义突变比核心基因多，这可能反映了 PAV 的有效种群规模较小，以及由于基因丢失的净化效应而带来的适应性优势。我们的结果表明，在野生范围扩张期间，泛基因组发生了收缩。选择信号提供了证据，表明部分或完全基因丢失是普通菜豆群体的一个关键适应性遗传变化，对植物适应具有重要意义。泛基因组是粮食豆类研究和适应气候变化及可持续农业的重要资源。
