Draft Genome Assembly of the Ancient Tetraploid Orphan Legume Marama Bean (Tylosema esculentum) with PacBio HiFi data

Abstract

AbstractTylosema esculentum(marama bean), an underutilized orphan legume, has long been considered to have the potential to be domesticated as a crop to improve local food security due to the nutrient-rich seeds. As a plant species that grows naturally in the deserts of southern Africa, marama also serves as a good model for studying plant adaptation to extreme environments. In this study, HMW leaf DNA samples were prepared to generate 21.6 Gb PacBio HiFi data, which was assembled into to a raw tetraploid genome assembly of 1.24 Gb using Canu and into a partially phased assembly of 564.8 Mb by Hifiasm. The N50 values were 1.28 Mb and 2.75 Mb, respectively, and the BUSCO completeness were all above 99%. Repeats were found to account for 27.35% of the genome. The k-mer analysis indicated that marama was likely to be an autotetraploid plant with an estimated haplotype genome size of only 277 Mb. The current assembly was aligned with the genome ofBauhinia variegata, the closest species to marama whose genome has been sequenced, with an overall alignment rate of only 20.36% indicating a significant divergence between the two. This is the first high-quality genome assembly of marama bean, albeit unphased and still fragmented. However, some of the long contigs, which can be close to half the chromosome length, can serve as good references for studying the genes underlying the traits of interest. This will greatly facilitate the molecular breeding of the bean.