ArticleBMC bioinformatics2019
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Genome reshaping by Helitron transposons in Fusarium oxysporum TR4 affects secondary metabolism but not virulence.Nature communications · 2026Article
- Three Near telomere-to-telomere Genomes for Gardenia jasminoides.Scientific data · 2026Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Article
- Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.Communications biology · 2024Article
- Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO.Nucleic acids research · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed.The plant genome · 2024Article
- The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism.Heliyon · 2024Article
- Maternal dominance contributes to subgenome differentiation in allopolyploid fishes.Nature communications · 2023Article
- tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana.BMC plant biology · 2023Article
- RepBox: a toolbox for the identification of repetitive elements.BMC bioinformatics · 2023Article
- Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes.Functional & integrative genomics · 2023Article
- Abundance of Transgene Transcript Variants Associated with Somatically Active TransgenicInternational journal of molecular sciences · 2023Article
- Chromosome-scale assemblies ofFrontiers in plant science · 2023Article
- Insights from the genomes of 4 diploid Camelina spp.G3 (Bethesda, Md.) · 2022Article
- A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.The Plant cell · 2022Article
- High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens.Microbiology spectrum · 2022Article
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Authors and funding
9 authors.
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Abstract
backgroundHelitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.
resultsWe developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes.
conclusionEAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.
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