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Yam bean (Pachyrhizus erosus Rich. Ex DC.) is an underutilized leguminous crop which has been used as a food source across central America and Asia. It is adapted to a range of environments and is closely related to major leguminous food crops, offering the potential to understand the genetic basis of environmental adaptation, and it may be used as a source of novel genes and alleles for the improvement of other legumes. Here, we assembled a draft genome of P. erosus of 460 Mbp in size containing 37,886 gene models. We used this assembly to compare three cultivars each of P. erosus and the closely related P. tuberosus and identified 10,187,899 candidate single nucleotide polymorphisms (SNPs). The SNP distribution reflects the geographic origin and morphology of the individuals.