ArticleProceedings of the National Academy of Sciences of the United States of America2006
Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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126 citing papers in PubMed, 291 citations in OpenAlex.
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- Host Factors Promoting the LTR Retrotransposon Life Cycle in Plant Cells: Current Knowledge and Future Directions.International journal of molecular sciences · 2025Review
- Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.Genome biology · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- Extensive genome evolution distinguishes maize within a stable tribe of grasses.bioRxiv : the preprint server for biology · 2025Article
- GABA does not regulate stomatal CO2 signalling in Arabidopsis.Journal of experimental botany · 2024Article
- Species of the SectionsInternational journal of molecular sciences · 2024Review
- Whole genome resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.).Journal, genetic engineering & biotechnology · 2024Article
- Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.PLoS genetics · 2023Article
- Short Interrupted Repeat Cassette (SIRC)-Novel Type of Repetitive DNA Element Found inInternational journal of molecular sciences · 2023Article
- Article
- Transposase expression, element abundance, element size, and DNA repair determine the mobility and heritability ofFrontiers in cell and developmental biology · 2023Article
- Integration of Repeatomic and Cytogenetic Data on Satellite DNA for the Genome Analysis in the GenusPlants (Basel, Switzerland) · 2022Article
- Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.EMBO reports · 2022Article
- Integration of Genomic and Cytogenetic Data on Tandem DNAs for Analyzing the Genome Diversity Within the GenusFrontiers in plant science · 2022Article
- Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines.Frontiers in plant science · 2022Article
- Phenotypic and Methylome Responses to Salt Stress inFrontiers in plant science · 2022Article
- Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity ofInternational journal of molecular sciences · 2021Article
- Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae.Genome biology and evolution · 2021Article
66 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of LTR retrotransposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with >10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with >1,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were >1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat Triticum monococcum and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages.
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