ArticleJournal of molecular evolution2009
The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana.
Article in Journal of molecular evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 74 citations in OpenAlex.
- A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.Plant communications · 2026Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity ofPlants (Basel, Switzerland) · 2024Article
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons.Frontiers in plant science · 2023Article
- The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity.The New phytologist · 2022Article
- Transposable Elements in the Revealing of Polymorphism-Based Differences in the Seeds of Flax Varieties Grown in Remediated Chernobyl Area.Plants (Basel, Switzerland) · 2022Article
- Review
- Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity ofInternational journal of molecular sciences · 2021Article
- CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species.PloS one · 2021Article
- Distribution and Characteristics of Transposable Elements in the Mulberry Genome.The plant genome · 2019Article
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- The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.Nucleic acids research · 2018Article
- Domestication of rice has reduced the occurrence of transposable elements within gene coding regions.BMC genomics · 2017Article
- Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.BMC genomics · 2016Article
- Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana.Nucleic acids research · 2015Article
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
The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes.
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