ArticleNature communications2025
Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Review
- Transposable elements and their epigenetic modifications mediate gene expression and subgenome dominance in Brassica carinata.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pangenome and Pan-Transcriptome Analysis of theEcology and evolution · 2026Article
- Repeatome divergence and recent LTR retrotransposon dynamics in phylogenetically diverse medicinal plant genomes.Genetica · 2026Article
- Article
- The genetic heist: how transposable elements capture and repurpose genes in plants.Genome biology · 2026Review
- The receptor-like pseudokinase LENG stimulates chilling tolerance in rice by inhibiting the activity of the OsCRPK1-OsGF14d module.Journal of integrative plant biology · 2026Article
- A Pan-TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Molecular mechanisms of plant freezing tolerance: from cold signal perception to adaptive responses.Frontiers in plant science · 2026Review
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Authors and funding
15 authors.
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Abstract
Transposable elements (TEs) introduce genetic and epigenetic variability, contributing to gene expression patterns that drive adaptive evolution in plants. Here, we investigate TE architecture and its effect on cold tolerance in rice. By analyzing a pangenome graph and the resequencing data of 165 rice accessions, we identify 30,316 transposable element insertion polymorphism (TIP) sites, highlighting significant diversity among polymorphic TEs (pTEs). We observe that pTEs exhibit increased H3K27me3 enrichment, suggesting a potential role in epigenetic differentiation under cold stress and in the transcriptional regulation of the cold response. We identify 26,914 TEs responsive to cold stress from transcriptome data, indicating their potential significance in regulatory networks for this response. Our TIP-GWAS analysis reveal two cold tolerance genes OsCACT and OsPTR. The biological functions of these genes are confirmed using knockout and overexpression lines. Our web tool ( https://cbi.gxu.edu.cn/RICEPTEDB/ ) makes all pTEs available to researchers for further analysis. These findings provide valuable targets for breeding cold-tolerant rice varieties, indicating the potential importance of pTEs in crop enhancement.
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