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

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.