Selection signatures and population dynamics of transposable elements in lima bean.

Autor: Lozano-Arce D; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia., García T; Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia., Gonzalez-Garcia LN; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.; Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France., Guyot R; Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France., Chacón-Sánchez MI; Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia., Duitama J; Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia. ja.duitama@uniandes.edu.co.
Jazyk: angličtina
Zdroj: Communications biology [Commun Biol] 2023 Aug 02; Vol. 6 (1), pp. 803. Date of Electronic Publication: 2023 Aug 02.
DOI: 10.1038/s42003-023-05144-y
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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