ArticleNucleic acids research2017
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 233 papers.
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233 citing papers in PubMed, 331 citations in OpenAlex.
- Genome evolution of Mediterranean olives following DNA repeats diversification.The plant genome · 2026Article
- Cross-species incompatibilities offer new insights into the functional consequences of satellite DNA evolution.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Review
- Molecular divergence and genomic composition of B chromosomes in the fish Cyphocharax modestus (Characiformes, Curimatidae).Scientific reports · 2026Article
- Satellite DNAs in Drosophila koepferae (repleta group) reveal patterns of origin, chromosomal organization, transcription, and turnover in the buzzatii cluster.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Technologies for engineering repetitive DNA.Quantitative biology (Beijing, China) · 2026Review
- Detailed re-analysis of satellitome mapping facilitated by the telomere-to-telomere (T2T) assembly of bread wheat genome.Plant molecular biology · 2026Article
- Comparative Analysis of Triticeae Satellite Repeats Using Low-Coverage Sequencing, qPCR, and FISH.International journal of molecular sciences · 2026Article
- Article
- Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes.Heredity · 2026Article
- Satellite DNA evolution in two holocentric species of Edessa true bugs (Hemiptera: Pentatomidae) with unusually high heterochromatin abundance.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Satellite DNA sequence dictates pericentromere heterochromatin formation and function.Science advances · 2026Article
- Unconventional centromere architectures in Tapirus indicus reveal hotspots for satellite-free centromere formation in Perissodactyla.Communications biology · 2026Article
- Centromeric tandem repeats expansions in plateau zokor enhance chromosome stability for high-altitude adaptation.Genome biology · 2026Article
- Article
- Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects.bioRxiv : the preprint server for biology · 2026Article
- Genomic and ecological drivers of parallel arid adaptation in tree grapes (Vitaceae).Nature communications · 2026Article
- Nuclear genome profiling of two species ofNAR genomics and bioinformatics · 2026Article
- Integrative satellitomics reveals distinct patterns of organization, transcription and evolution of satellite DNAs in Tenebrio molitor.Biology direct · 2026Article
- The extraordinary satellitome diversity of freshwater crayfish: a driver of genome evolution.Mobile DNA · 2026Article
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
173 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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