Draft genome assembly of a domesticated Andean Lima bean accession

Abstract

The genus Phaseolus has a rich domestication history as five species have been domesticated. In particular, the domestication process in Lima bean \textit{Phaseolus lunatus} involves at least two independent domestication events. Each of them started from different genetic pools, Mesoamerican and Andean, and converged into similar phenotypes, making the Lima bean an ideal opportunity to understand convergent evolution in domestication. However, until now, the lack of a high-quality reference genome of the Andean genetic lineage has hampered progress in downstream analysis, including genetic and functional genomics studies. \\ In this study, we conducted a high-quality genome assembly of the domesticated Andean Lima bean, resulting in a total genome size of 597.70 Mbp. The assembly exhibited high completeness, with 98.7% of BUSCO genes detected. The assembly consisted of 1070 contigs, with an N50 value of 8.71 Mbp and about 39% of TEs mainly in the form of LTR retrotransposons. We concluded that our assembly increased genome size was primarily attributed to the proliferation of the GYPSY/TAT lineage through recent insertions. Additionally, a whole-genome alignment revealed strong macrosynteny and consistency among the assemblies. Yet, it unveiled numerous structural variations between two individuals of the same species, especially extensive inversions in various chromosomes. These findings provide insights into the genome characteristics and structural variations of this bean species, contributing to our understanding of its genetic composition and evolutionary dynamics. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses, and genome-assisted breeding research.