Selection signatures and population dynamics of transposable elements in lima bean

Generation of a complete catalog of transposable elements in the lima bean genome provides insight into the two independent domestication events that occurred in the Mesoamerican and Andean gene pools of this species. The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.

Automated summary

The complete catalog of transposable elements in the lima bean genome sheds light on the dual domestication events in the Mesoamerican and Andean gene pools. These events make lima bean an ideal model for studying convergent evolution. The mechanisms of adaptation and the genes involved in these processes are not well understood, and this study demonstrates the potential role of transposable elements in shaping gene functions. The analysis of whole-genome sequencing data reveals the genetic structure of lima bean and provides insights into its demographic history and selection processes during domestication.