Genome assembly and population analysis of tetraploid Tylosema esculentum (marama) reveal two district genomes.

Abstract Tylosema esculentum (marama bean), is an underutilized orphan legume with potential for domestication as a food crop to improve local food security. Thriving in the desert environments of southern Africa, it offers insights into plant adaptation to extreme conditions. In this study, 21.6 Gb PacBio HiFi data were assembled into a tetraploid genome of 1.24 Gb using Canu, achieving an N50 of 1.28 Mb and over 99% BUSCO completeness. Repeats constituted 27.35% of the genome. k-mer analysis suggested an autotetraploid or ancient allotetraploid genome for marama, with a compact haplotype genome size of 277 Mb. Phylogenetic analysis revealed a close relationship to Bauhinia variegata, diverging approximately 25.14 million years ago (MYA). Whole genome duplication (WGD) analysis indicated an ancient duplication event in marama. Enriched species-specific genes were involved in DNA processes, protein functions, and stress response pathways, highlighting their potential roles in marama’s adaption to diverse environments. The population study identified two distinct clusters, but additional phenotyping is required to assess whether these genomic differences are reflected in biological performance. This is the first high-quality genome assembly of marama, albeit unphased, represents a significant advancement in understanding marama's genomics.