ArticlePloS one2014
Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter.
Article in PloS one, 2014. 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.
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- Taxonomy, Phylogeny, Genomes, and Repeatomes in the SubgeneraInternational journal of molecular sciences · 2025Review
- Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library.BMC genomics · 2025Article
- Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes.BMC genomic data · 2025Article
- Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.Mobile DNA · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Comparative Analysis of Active LTR Retrotransposons in Sunflower (International journal of molecular sciences · 2024Article
- The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes.Plants (Basel, Switzerland) · 2023Article
- Making the Genome Huge: The Case ofGenes · 2023Article
- Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species ofInternational journal of molecular sciences · 2023Article
- Review
- DNA methylation across the tree of life, from micro to macro-organism.Bioengineered · 2022Article
- Repeatome-Based Phylogenetics in Pelargonium Section Ciconium (Sweet) Harvey.Genome biology and evolution · 2021Article
- Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.The Plant journal : for cell and molecular biology · 2021Article
- Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries.Scientific reports · 2020Article
- Satellitome Analysis in the Ladybird BeetleGenes · 2020Article
- The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy.Genes & genomics · 2020Review
- Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically DistinctGenes · 2020Article
- Characterization and Dynamics of Repeatomes in Closely Related Species ofFrontiers in plant science · 2020Article
- Twenty years of transposable element analysis in theMobile DNA · 2020Review
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Abstract
Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and non-annotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the A. thaliana repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant.
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