ArticleGenome research2009
Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species.Frontiers in plant science · 2026Article
- Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).Genome biology · 2025Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Lepidopteran Genomes Have Denser Transposable Elements in Smaller Chromosomes, Likely Driven by Non-allelic Homologous Recombination.Genome biology and evolution · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica-indica subspecies.Nature plants · 2025Article
- Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.Mobile DNA · 2025Article
- Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.Genome biology and evolution · 2024Article
- Patterns of Chromosomal Variation, Homoeologous Exchange, and Their Relationship with Genomic Features in Early Generations of a Synthetic Rice Segmental Allotetraploid.International journal of molecular sciences · 2023Article
- The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.The Plant journal : for cell and molecular biology · 2022Article
- Methylation in the CHH Context Allows to Predict Recombination in Rice.International journal of molecular sciences · 2022Article
- The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments.Molecular biology and evolution · 2022Article
- Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Mutation Load in Sunflower Inversions Is Negatively Correlated with Inversion Heterozygosity.Molecular biology and evolution · 2022Article
- Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress.Frontiers in plant science · 2022Review
- Genome Size Variation and Evolution Driven by Transposable Elements in the GenusFrontiers in plant science · 2022Article
- Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum).Genome biology and evolution · 2021Article
- Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation.Genome biology · 2021Article
- The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality.Genome biology and evolution · 2021Article
35 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.
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