Selection signatures and population dynamics of transposable elements in lima bean
Abstract 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 landrace...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-08-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-05144-y |
| _version_ | 1797752644765220864 |
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| author | Daniela Lozano-Arce Tatiana García Laura Natalia Gonzalez-Garcia Romain Guyot Maria Isabel Chacón-Sánchez Jorge Duitama |
| author_facet | Daniela Lozano-Arce Tatiana García Laura Natalia Gonzalez-Garcia Romain Guyot Maria Isabel Chacón-Sánchez Jorge Duitama |
| author_sort | Daniela Lozano-Arce |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-12T17:07:30Z |
| format | Article |
| id | doaj.art-c7dc0fdbc362490097c101308f55a31c |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-12T17:07:30Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-c7dc0fdbc362490097c101308f55a31c2023-08-06T11:22:32ZengNature PortfolioCommunications Biology2399-36422023-08-016111310.1038/s42003-023-05144-ySelection signatures and population dynamics of transposable elements in lima beanDaniela Lozano-Arce0Tatiana García1Laura Natalia Gonzalez-Garcia2Romain Guyot3Maria Isabel Chacón-Sánchez4Jorge Duitama5Systems and Computing Engineering Department, Universidad de los AndesDepartamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaSystems and Computing Engineering Department, Universidad de los AndesInstitut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRADDepartamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de ColombiaSystems and Computing Engineering Department, Universidad de los AndesAbstract 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.https://doi.org/10.1038/s42003-023-05144-y |
| spellingShingle | Daniela Lozano-Arce Tatiana García Laura Natalia Gonzalez-Garcia Romain Guyot Maria Isabel Chacón-Sánchez Jorge Duitama Selection signatures and population dynamics of transposable elements in lima bean Communications Biology |
| title | Selection signatures and population dynamics of transposable elements in lima bean |
| title_full | Selection signatures and population dynamics of transposable elements in lima bean |
| title_fullStr | Selection signatures and population dynamics of transposable elements in lima bean |
| title_full_unstemmed | Selection signatures and population dynamics of transposable elements in lima bean |
| title_short | Selection signatures and population dynamics of transposable elements in lima bean |
| title_sort | selection signatures and population dynamics of transposable elements in lima bean |
| url | https://doi.org/10.1038/s42003-023-05144-y |
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