Recent evolution, domestication and metabolism of cyanide compounds in Lima bean

Abstract

<title>Abstract</title> The evolution and functional genomics of the biosynthesis of secondary metabolites, including production of hydrogen cyanide (HCN), is a major goal in Lima bean research. This work describes our latest findings in short time evolution, genomics and expression, applied to Lima bean. This includes a chromosome-level assembly for the Andean gene pool and long-read sequencing of wild relatives. Large indels explained by transposable elements affect promoter regions of several genes related to domestication traits. The two major gene pools of P. lunatus diverged within the last million years, but recent insertions of LTRs produced important variations in genome size and composition. A core metabolic network for Phaseolus revealed patterns of variability in RNA expression for genes related to different primary and secondary metabolic processes. The Phaseolus genomes have important differences in the number, location, and expression of genes, which can explain the unique ability of Lima bean across domesticated Phaseolus species for production of HCN.