ArticleMobile DNA2017
The repetitive landscape of the 5100 Mbp barley genome.
Article in Mobile DNA, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 69 citations in OpenAlex.
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- Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly.Nature communications · 2026Article
- Transposable element dynamics drive rapid evolution of centromere architecture in the Avena genus.Genome biology · 2026Article
- Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species.Molecular biology and evolution · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Do duplication-inducing elements 'cooperate' with genes in evolutionary arms races? A case study on cereal crop pathogenesis.BMC plant biology · 2025Article
- Core promoterome of barley embryo.Computational and structural biotechnology journal · 2024Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons.Mobile DNA · 2024Article
- Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding.BMC genomics · 2023Article
- A survey of lineage-specific genes inPlant direct · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- The nature and organization of satellite DNAs inFrontiers in plant science · 2023Article
- Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons.Advanced genetics (Hoboken, N.J.) · 2022Article
- Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype.iScience · 2022Article
- Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages.Frontiers in plant science · 2022Article
- Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad-spectrum resistance.The plant genome · 2021Article
- CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation.Genome biology and evolution · 2021Article
- Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley.International journal of molecular sciences · 2021Article
- The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth.The plant genome · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 10 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated.
resultsHere, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low copy numbers. We found that the barley genome is highly compartmentalized with different types of TEs occupying different chromosomal "niches", such as distal, interstitial, or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Furthermore, their presence in gene promoters is associated with decreased methylation levels.
conclusionsOur data show that TEs are major determinants of overall chromosome structure. We hypothesize that many of the the various chromosomal distribution patterns are the result of TE families targeting specific niches, rather than them accumulating where they have the least deleterious effects.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.