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image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
New Phytologist
Article . 2025 . Peer-reviewed
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New Phytologist
Article . 2025
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Genome‐wide patterns of local adaptation associated with transposable elements in Tetrastigma hemsleyanum (Vitaceae)

Authors: Chaoqian Ren; Hans Peter Comes; Shanshan Zhu; Xinyi Zhang; Weimei Jiang; Chengxin Fu; Jun Chen; +2 Authors

Genome‐wide patterns of local adaptation associated with transposable elements in Tetrastigma hemsleyanum (Vitaceae)

Abstract

Summary The mobility of transposable elements (TEs) partly drives genome evolution, potentially leading to either adaptive or deleterious effects. However, it remains far from clear whether and how TEs contribute to adaptation to changing environments, especially in plants. We analyzed whole‐genome sequencing data from 29 ecologically diverse Tetrastigma hemsleyanum populations to infer the species' demographic history and its impact on TE polymorphisms. Integrated selective sweep and genome–environment association (GEA) approaches were employed to examine the contribution of TEs to environmental adaptation. The ancestor of T. hemsleyanum diverged during the late Miocene/Pliocene, forming two lineages that further split into four sublineages. These (sub)lineages underwent periodic population declines and recoveries during the late‐Pleistocene climatic oscillations, with most polymorphic TEs transposing during the last glacial period. A small fraction of these TEs (0.033–0.40%) showed signatures of positive selection, while a broader subset (0.081–0.76%) correlated significantly with climatic variables. Notably, these selected or climate‐linked TE polymorphisms were preferentially retained in gene‐poor regions and frequently linked to genes involved in organ development and stress/defense response. Our findings demonstrate that TEs played a key regulatory and adaptive role in T . hemsleyanum 's response to environmental change, underscoring their importance in better understanding the genomic mechanisms underlying adaptation.

Related Organizations
Keywords

Polymorphism, Genetic, Vitaceae, DNA Transposable Elements, Selection, Genetic, Adaptation, Physiological, Genome, Plant, Phylogeny

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
3
Top 10%
Average
Average
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