ArticleGenome biology2014
Organization and evolution of transposable elements along the bread wheat chromosome 3B.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 123 citations in OpenAlex.
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- Ancient Whole-Genome Duplication and Lineage-Specific Retention Shape the Diversification of bZIP Transcription Factors in Pooideae.Plants (Basel, Switzerland) · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
- Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.Genome biology · 2025Article
- Lepidopteran Genomes Have Denser Transposable Elements in Smaller Chromosomes, Likely Driven by Non-allelic Homologous Recombination.Genome biology and evolution · 2025Article
- Transposable elements drive the subgenomic divergence of homoeologous genes to shape wheat domestication and improvement.Plant communications · 2025Article
- A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.Nature genetics · 2025Article
- Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome.Genome biology · 2025Article
- Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement.Plant communications · 2025Article
- Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement.Plant biotechnology journal · 2024Article
- Wheat MYOSIN-RESEMBLING CHLOROPLAST PROTEIN controls B-type starch granule initiation timing during endosperm development.Plant physiology · 2024Article
- Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- An integrated strategy involving high-throughput sequencing to characterize an unknown GM wheat event in Canada.Plant biotechnology journal · 2024Article
- Activation characteristics of Ty3-retrotransposons after spaceflight and genetic stability of insertion sites in rice progeny.Frontiers in plant science · 2024Article
- Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat.Nature communications · 2023Article
- Chromosome level genome assembly of colored calla lily (Zantedeschia elliottiana).Scientific data · 2023Article
- All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity.The plant genome · 2023Article
- A survey of lineage-specific genes inPlant direct · 2023Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far.
resultsWe develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.
conclusionAccurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
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