ArticleGenome research2004
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 271 papers.
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Who cites it
271 citing papers in PubMed, 549 citations in OpenAlex.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Loss-of-function of MIR172b and prime editing of SNB reveal a regulatory module underlying cleistogamy in rice.Plant physiology · 2026Article
- Nuclear genome profiling of two species ofNAR genomics and bioinformatics · 2026Article
- Novel insights into retrogene evolution and cold adaptation in the alpine plant Crucihimalaya himalaica (Brassicaceae).BMC biology · 2026Article
- Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).Genome biology · 2025Article
- Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.Genomics, proteomics & bioinformatics · 2025Article
- The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum.Plants (Basel, Switzerland) · 2025Article
- Article
- Homoploid hybridization adds clarity to the origins of octoploid strawberries.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.Mobile DNA · 2025Article
- A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum.BMC plant biology · 2024Article
- Chromosome-scale genome assembly of sweet tea (Lithocarpus polystachyus Rehder).Scientific data · 2023Article
- Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.PLoS genetics · 2023Article
- Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice.Nature genetics · 2023Article
- Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species.BMC genomics · 2023Article
- The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods.PLoS genetics · 2023Article
- The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes.Plants (Basel, Switzerland) · 2023Article
- Insights into mammalian TE diversity through the curation of 248 genome assemblies.Science (New York, N.Y.) · 2023Article
211 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We initially analyzed 11 families of low- and middle-copy-number long terminal repeat (LTR) retrotransposons in rice to determine how their structures have diverged from their predicted ancestral forms. These elements, many highly fragmented, were identified on the basis of sequence homology and structural characteristics. The 11 families, totaling 1000 elements, have copy numbers ranging from 1 to 278. Less than one-quarter of these elements are intact, whereas the remaining are solo LTRs and variously truncated fragments. We also analyzed two highly repetitive families (Osr8 and Osr30) of LTR retrotransposons and observed the same results. Our data indicate that unequal homologous recombination and illegitimate recombination are primarily responsible for LTR-retrotransposon removal. Further analysis suggests that most of the detectable LTR retrotransposons in rice inserted less than 8 million years ago, and have now lost over two-thirds of their encoded sequences. Hence, we predict that the half-life of LTR-retrotransposon sequences in rice is less than 6 million years. Moreover, our data demonstrate that at least 22% (97 Mb) of the current rice genome is comprised of LTR-retrotransposon sequences, and that more than 190 Mb of LTR-retrotransposon sequences have been deleted from the rice genome in the last 8 million years.
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