ArticleMobile DNA2019
Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification.
Article in Mobile DNA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 258 papers.
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Who cites it
258 citing papers in PubMed.
- Genome evolution of Mediterranean olives following DNA repeats diversification.The plant genome · 2026Article
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly.Nature communications · 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
- A single species, different repeatomes? Genomic plasticity in Passiflora foetida L. complex and comparative insights across the subgenus Passiflora.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Repeatome divergence and recent LTR retrotransposon dynamics in phylogenetically diverse medicinal plant genomes.Genetica · 2026Article
- Integrated Comparative Genomics and Population Genomics Reveal the Genomic and Epigenomic Basis of Barley (Plants (Basel, Switzerland) · 2026Article
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- A Chromosome-Scale Genome Assembly and Annotation of the Antarctic Pearlwort Colobanthus quitensis (Caryophyllaceae).Genome biology and evolution · 2026Article
- Transposable element dynamics drive rapid evolution of centromere architecture in the Avena genus.Genome biology · 2026Article
- Nuclear genome profiling of two species ofNAR genomics and bioinformatics · 2026Article
- The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean.Nature communications · 2026Article
- Whole-genome sequencing revealed the genomic origin of Solanum demissum Lindl., a Mexican hexaploid wild potato species.BMC plant biology · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Telomere-to-telomere genome assembly and a mutant library empower functional genomics and genetic improvement in Cucurbita moschata.Plant communications · 2026Article
- Comparative Transcriptomics Reveals an Extracellular Worm Argonaute as an Ancestral Regulator of LTR Retrotransposons.Genome biology and evolution · 2026Article
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
- A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of theInternational journal of molecular sciences · 2026Article
- Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.Mobile DNA · 2026Article
198 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
backgroundPlant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons.
resultsWe have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains.
conclusionsWe have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/).
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