ArticleGenome biology2002
Long terminal repeat retrotransposons of Oryza sativa.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 139 citations in OpenAlex.
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- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Genome Size Variation and Evolution Driven by Transposable Elements in the GenusFrontiers in plant science · 2022Article
- Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi.BMC genomics · 2021Article
- Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for thePlants (Basel, Switzerland) · 2021Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
- Evolutionary patterns of chimeric retrogenes in Oryza species.Scientific reports · 2019Article
- Article
- Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice.Molecular biology and evolution · 2018Article
- Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-GenomeG3 (Bethesda, Md.) · 2017Article
- Recent amplification of Osr4 LTR-retrotransposon caused ricePlant diversity · 2017Article
- Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons inFrontiers in plant science · 2017Article
- In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.Bioinformatics and biology insights · 2017Article
- A new look at the LTR retrotransposon content of the chicken genome.BMC genomics · 2016Article
- Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome.BMC plant biology · 2016Article
- Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza.Evolutionary bioinformatics online · 2016Article
- Article
- RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions.BMC plant biology · 2014Article
- LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.Mobile DNA · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLong terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes.
resultsUsing a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons.
conclusionsEach of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover.
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