ArticleBMC bioinformatics2010
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 261 papers, 1 of them a synthesis that pooled it.
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Who cites it
261 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
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- Identification of highly immunogenic endogenous dsRNAs from cellular MDA5 filaments.bioRxiv : the preprint server for biology · 2026Article
- A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of theInternational journal of molecular sciences · 2026Article
- Evolutionary genomics and divergence of Cacopsylla species with a special focus on the apple proliferation vectors Cacopsylla melanoneura and Cacopsylla picta.BMC genomics · 2026Article
- Emergence of satellite DNAs suggests centromeric repositioning as a driver of karyotypic variation of the freshwater darter characines (Apareiodon affinis).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Cytogenomics of the Flea BeetleGenes · 2026Article
- The Repeatome in the Mega-GenusGenes · 2026Article
- The repeatome landscape in the "Frontiers in plant science · 2026Article
- REAPER: a project-centric workflow layer for comparative repeatome analysis.Frontiers in plant science · 2026Article
- Kinetochore mutations and histone phosphorylation pattern changes accompany holo- and macro-monocentromere evolution.Nature communications · 2025Article
- Dynamics of repetitive DNA sequences over the course of evolution and intraspecific divergence of tetraploid goat-grass species Aegilops biuncialis vis.BMC plant biology · 2025Article
- Development of wheat D genome-specific molecular markers based on subgenome-specific repeats.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Satellite DNA Genomics: The Ongoing Story.International journal of molecular sciences · 2025Review
- Investigating the evolution of large meiotic rings of multiple X and Y sex chromosomes in two Leptodactylus frog species (Anura, Leptodactylidae).Communications biology · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Expansion of satellite DNAs derived from transposable elements in beetles with reduced diploid numbers.Heredity · 2025Article
- Article
201 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization.
resultsWe adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families.
conclusionsRepetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences.
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