ArticleGenome biology2016
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 62 citations in OpenAlex.
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- The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.Molecular biology and evolution · 2024Article
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- Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes.Molecular biology and evolution · 2024Article
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- Identification of transcriptionally active transposons in Barley.BMC genomic data · 2023Article
- Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton.Science China. Life sciences · 2023Article
- Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen.PLoS pathogens · 2023Article
- A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease.Mobile DNA · 2022Article
- Ovule siRNAs methylate protein-coding genes in trans.The Plant cell · 2022Article
- Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser.Genome biology and evolution · 2022Article
- TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- Transposable element variants and their potential adaptive impact in urban populations of the malaria vectorGenome research · 2022Article
- Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii.Nucleic acids research · 2021Article
- Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability.Annals of botany · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTerminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.
resultsUsing a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa.
conclusionsWe perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.
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