ArticleNature communications2019
Retrotranspositional landscape of Asian rice revealed by 3000 genomes.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 158 citations in OpenAlex.
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- The jujube pan-TE map identifies transposable element insertions associated with domestication and pericarp development.Horticulture research · 2026Article
- Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.Nature communications · 2026Article
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.BMC genomics · 2026Article
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- Genomic insights into genome-wide heterozygosity and its impact on walnut adaptive evolution and improvement.Molecular breeding : new strategies in plant improvement · 2025Article
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice.Frontiers in plant science · 2025Article
- Reverse Mutations in Pigmentation Induced by Sodium Azide in the IR64 Rice Variety.Current issues in molecular biology · 2024Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata).BMC genomics · 2024Article
- Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits.Nature communications · 2024Article
- A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.National science review · 2024Article
- Article
- A Novel Allele in the Promoter ofPlants (Basel, Switzerland) · 2024Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- A syntelog-based pan-genome provides insights into rice domestication and de-domestication.Genome biology · 2023Article
- Transposons are important contributors to gene expression variability under selection in rice populations.eLife · 2023Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.