ArticleProceedings of the National Academy of Sciences of the United States of America2014
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 169 papers.
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169 citing papers in PubMed.
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- Systematic prioritization of candidate genes in camptothecin biosynthesis using multi-omics and deep learning.The plant genome · 2026Article
- 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
- Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida).Scientific data · 2026Article
- Regulatory Logic and Transposable Element Dynamics in Caenorhabditis Genomes.Genome biology and evolution · 2026Article
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- Evolution and diversification of PAL-mediated salicylic acid biosynthesis in Rosaceae.Horticulture research · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- A structurally unique effector shared between vascular wilt fungi drives cotton and olive defoliation.Nature communications · 2026Article
- Distinct genomic architectures but the same gene underlie the convergent evolution of a plant supergene.Science advances · 2026Article
- A highly contiguous chromosome-level genome assembly of the Chilean jack mackerel Trachurus murphyi.Scientific data · 2026Article
- An active Helitron transposon family in wheat.Nature plants · 2026Article
- Chromosome-level genome ofiScience · 2026Article
- De Novo Chromosome-Level Genome Assembly of 'Qing Zhou Mi' Landrace Peach and Analysis of Late Maturity and Fruit Weight Traits in Peach.Plants (Basel, Switzerland) · 2026Article
- The chromosome-scale genome assembly and annotation of Rosa bracteata (Macartney Rose).Scientific data · 2026Article
- First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.G3 (Bethesda, Md.) · 2026Article
- A chromosomal haplotype-resolved genome assembly of Cuphea hookeriana.Scientific data · 2026Article
- Chromosome-level genome assembly and annotation of the tropical sea cucumber Holothuria fuscocinerea.Scientific data · 2026Article
109 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner's predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5' and 3' termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.
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