ArticleNAR genomics and bioinformatics2024
DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 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
- The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean.Nature communications · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Allelic variation at a single locus distinguishes spring and winter faba beans.Nature genetics · 2026Article
- Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- The repeatome landscape in the "Frontiers in plant science · 2026Article
- First draft genome of the decaploid species,GigaByte (Hong Kong, China) · 2026Article
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
- Positive-Strand RNA Viruses Induce LTR Retrotransposon Transcription and Extrachromosomal Circular DNA Generation in Plants.International journal of molecular sciences · 2025Article
- Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes.Genome biology · 2025Article
- The maize B chromosome shapes the transcriptome throughout the entire plant life cycle.Journal of experimental botany · 2025Article
- Rebalancing the seed proteome following deletion of vicilin-related genes in pea (Pisum sativum L.).Journal of experimental botany · 2025Article
- Comparative Analysis of Chromosome Repeat DNA Patterns in FourInternational journal of molecular sciences · 2025Article
- Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream.Genomics, proteomics & bioinformatics · 2025Article
- Integration of Repeatome and Cytogenetic Data on Tandem DNAs in a Medicinal PlantInternational journal of molecular sciences · 2025Article
- Dynamic patterns of repeats and retrotransposons in the centromeres of Humulus lupulus L.The New phytologist · 2025Article
- Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution.The New phytologist · 2025Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long terminal repeat (LTR) retrotransposons constitute a predominant class of repetitive DNA elements in most plant genomes. With the increasing number of sequenced plant genomes, there is an ongoing demand for computational tools facilitating efficient annotation and classification of LTR retrotransposons in plant genome assemblies. Herein, we introduce DANTE, a computational pipeline for Domain-based ANnotation of Transposable Elements, designed for sensitive detection of these elements via their conserved protein domain sequences. The identified protein domains are subsequently inputted into the DANTE_LTR pipeline to annotate complete element sequences by detecting their structural features, such as LTRs, in adjacent genomic regions. Leveraging domain sequences allows for precise classification of elements into phylogenetic lineages, offering a more granular annotation compared with coarser conventional superfamily-based classification methods. The efficiency and accuracy of this approach were evidenced via annotation of LTR retrotransposons in 93 plant genomes. Results were benchmarked against several established pipelines, showing that DANTE_LTR is capable of identifying significantly more intact LTR retrotransposons. DANTE and DANTE_LTR are provided as user-friendly Galaxy tools accessible via a public server (https://repeatexplorer-elixir.cerit-sc.cz), installable on local Galaxy instances from the Galaxy tool shed or executable from the command line.
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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.