Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia.
Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
Nat Commun. 2021 Jan 29;12(1):702. doi: 10.1038/s41467-021-20921-1.
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.
利马豆（Phaseolus lunatus L.）是五种已驯化的菜豆作物之一，在从墨西哥到阿根廷的分布范围内表现出广泛的生态适应性。这些适应性使它成为一种很有前途的作物，可以在拉丁美洲和其他地区气候变化预测情景下提高粮食安全。在这项工作中，我们结合长读和短读测序技术以及来自双亲群体的密集遗传图谱，获得了利马豆的染色体水平基因组组装。对 28326 个基因模型的注释显示，与抗病性相关的保守结构域的 1917 个基因具有很高的多样性。与普通菜豆的 22180 个直系同源物的结构比较揭示了高度的基因组同线性和五个大的染色体内重排。群体基因组分析表明，野生利马豆分为六个聚类，分布区域大多不重叠，中美洲地方品种可进一步细分为三个亚聚类。RNA-seq 数据显示有 4275 个差异表达基因，这些基因可能与荚果开裂和种子发育有关。我们期望这里提供的资源能够为了解菜豆属物种在驯化过程中的趋同进化程度提供坚实的基础，并为适应气候变化的育种提供工具和信息。
