Selection signatures and population dynamics of transposable elements in Lima bean

The domestication process in Lima bean (Phaseolus lunatus L.) involves at least two independent events, within the Mesoamerican and Andean gene pools. Both processes produced similar phenotypic changes in landraces, making Lima bean an excellent model to understand convergent evolution. Despite recent research efforts, the mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. The genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Most of the previous genetic analyses in Lima bean have relied on Single Nucleotide Polymorphism (SNP) loci and have ignored transposable elements (TEs) which are a major source of variation in plant genomes. The current availability of high-throughput sequencing technologies enables the collection of whole-genome resequencing (WGS) data to approach intraspecies population dynamics of TEs. The present research collected WGS data from 60 wild and domesticated Lima bean accessions to generate the most complete characterization developed to date of transposable elements and SNP loci in the Lima bean genome. We generated an updated annotation of 223,780 transposable elements in the Lima bean genome. Furthermore, we identified genes and variable TEs affected by selective sweeps. Combining three different approaches, selective sweeps were predicted to generate a set of domestication candidate genes. A small percentage of genes under selection (1.6%) were shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. Up to 25% of the genes with previously reported selective sweeps in common bean were also detected in Lima bean. We also built a catalog of 39,459 TEs with presence-absence variation (PAV). The fact that 75% of these TEs were located close to genes shows their potential to affect gene functions in Lima bean. The genetic structure inferred from variable TEs was 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.