The Genome of the Lima Bean Variety Baiyu Bean Highlights Its Evolutionary Characteristics

The baiyu bean (<i>Phaseolus lunatus</i>), also known as the lima bean, is a plant belonging to the Fabaceae family, has a long and distinguished history of cultivation in China and is a highly regarded local variety of lima bean. In the current study, we present the reference genome of the baiyu bean variety, which has a scaffold N50 length of 47.545 Mb. A comparative genomic analysis was conducted using genomes of seven legume species, and the results demonstrated that 1564 and 1275 genes of baiyu bean exhibited expansion and contraction, respectively. Moreover, 543 genes were identified as exclusive to the baiyu bean. The analysis of adaptive evolution genes revealed the presence of 61 genes under adaptive evolution between <i>P. lunatus</i> and the common bean <i>P. vulgaris</i>. An examination of the branch model revealed the presence of five genes undergoing adaptive evolution in the <i>P. lunatus</i> branch. Additionally, the evolutionary selective pressure acting on other branches of legume plants was analyzed. A comprehensive analysis of structural variations (SVs) between the baiyu bean and G27455 genome was conducted, resulting in the identification of 5549 SVs. Among these, 333 genes were identified as high-impact SV genes. The acquisition of the genome sequence of this excellent variety will facilitate the exploration and utilization of its characteristics, providing a foundation for the genetic improvement of the lima bean.