The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly inves...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2024-04-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/93284 |
| _version_ | 1827287073666629632 |
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| author | Robert Horvath Nikolaos Minadakis Yann Bourgeois Anne C Roulin |
| author_facet | Robert Horvath Nikolaos Minadakis Yann Bourgeois Anne C Roulin |
| author_sort | Robert Horvath |
| collection | DOAJ |
| description | Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species. |
| first_indexed | 2024-04-24T10:50:47Z |
| format | Article |
| id | doaj.art-3856219ea0f540bdb30f2758b54ec73d |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-24T10:50:47Z |
| publishDate | 2024-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-3856219ea0f540bdb30f2758b54ec73d2024-04-12T11:25:20ZengeLife Sciences Publications LtdeLife2050-084X2024-04-011210.7554/eLife.93284The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor roleRobert Horvath0https://orcid.org/0000-0002-3221-8835Nikolaos Minadakis1Yann Bourgeois2https://orcid.org/0000-0002-1809-387XAnne C Roulin3https://orcid.org/0000-0002-6668-3321Department of Plant and Microbial Biology, University of Zurich, Zurich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zurich, Zurich, SwitzerlandDIADE, University of Montpellier, CIRAD, IRD, Montpellier, France; University of Portsmouth, Portsmouth, United KingdomDepartment of Plant and Microbial Biology, University of Zurich, Zurich, SwitzerlandUnderstanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.https://elifesciences.org/articles/93284brachypodium distachyonmodel grass speciespoaceae |
| spellingShingle | Robert Horvath Nikolaos Minadakis Yann Bourgeois Anne C Roulin The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role eLife brachypodium distachyon model grass species poaceae |
| title | The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role |
| title_full | The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role |
| title_fullStr | The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role |
| title_full_unstemmed | The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role |
| title_short | The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role |
| title_sort | evolution of transposable elements in brachypodium distachyon is governed by purifying selection while neutral and adaptive processes play a minor role |
| topic | brachypodium distachyon model grass species poaceae |
| url | https://elifesciences.org/articles/93284 |
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