ArticlePlant cell reports2012
Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains.
Article in Plant cell reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- qPCR as a Selective Tool for Cytogenetics.Plants (Basel, Switzerland) · 2022Article
- Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley.International journal of molecular sciences · 2021Article
- Development of SpecificInternational journal of molecular sciences · 2020Article
- Copy Number Variation of Transposable Elements inPlants (Basel, Switzerland) · 2019Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- Tracking the genome-wide outcomes of a transposable element burst over decades of amplification.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes.Genetics and molecular biology · 2017Article
- Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic.BMC plant biology · 2015Article
- Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing.PLoS genetics · 2014Article
- Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.The Plant journal : for cell and molecular biology · 2013Article
- Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization.Plant cell reports · 2013Article
- Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification.Plant physiology · 2013Article
- Mobilization of Stowaway-like MITEs in newly formed allohexaploid wheat species.Plant molecular biology · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number.
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