A chromosome-level reference genome of a Fabaceae species yam bean (Pachyrhizus erosus)

Abstract

Yam bean (Pachyrhizus erosusL.), belonging to the family Fabaceae, is an important but underutilized root crop. Here, we generated a high-quality chromosome-level reference genome of yam bean by PacBio HiFi and Hi-C sequencing, with assembly size of 539.0 Mb, contig N50 of 25.6 Mb, and BUSCO complete rate of 99.3%. Then, we anchored 94.4% of the contig sequences into 11 pseudo-chromosomes, and assembled the telomeres at 86.4% (19/22) of the chromosome-ends. A total of 44,692 protein-coding genes were predicted, with the BUSCO complete rate of 99.3%, comparable to that of the genome assembly. Compared to the previously reported yam bean genome, the current assembly has a 1,388-fold increase in contig N50 size, and 12.2% and 24.3% increase in BUSCO complete rate for the genome sequence and gene set, respectively. Evolutionary analysis revealed that yam bean diverged from the clade of soybean andPueraria lobatavar.montana22.5 MYA. This high-quality genome assembly will greatly facilitate the breeding of yam bean based on the genetic and genomic methods.