Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach

BackgroundDNA tandem repeats (TRs) are not just popular molecular markers, but are also important genomic elements from an evolutionary and functional perspective. For various genomes, the densities of short TR types were shown to differ strongly among different taxa and genomic regions. In this study we analysed the TR characteristics in the genomes of Daphnia pulex and 11 other eukaryotic species. Characteristics of TRs in different genomic regions and among different strands are compared in details for D. pulex and the two model insects Apis mellifera and Drosophila melanogaster.ResultsProfound differences in TR characteristics were found among all 12 genomes compared in this study. In D. pulex, the genomic density of TRs was low compared to the arthropod species D. melanogaster and A. mellifera. For these three species, very few common features in repeat type usage, density distribution, and length characteristics were observed in the genomes and in different genomic regions. In introns and coding regions an unexpectedly high strandedness was observed for several repeat motifs. In D. pulex, the density of TRs was highest in introns, a rare feature in animals. In coding regions, the density of TRs with unit sizes 7-50 bp were more than three times as high as for 1-6 bp repeats.ConclusionsTRs in the genome of D. pulex show several notable features, which distinguish it from the other genomes. Altogether, the highly non-random distribution of TRs among genomes, genomic regions and even among different DNA-stands raises many questions concerning their functional and evolutionary importance. The high density of TRs with a unit size longer than 6 bp found in non-coding and coding regions underpins the importance to include longer TR units in comparative analyses.

• Publication year

  2010

• Venue

  BMC Genomics

• Publication date

  2010-04-30

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/1471-2164-11-277PMID 20433735PMCID 3152781
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Daphnia as an emerging model for toxicological genomics

  2008cited by this paper
• Detecting Microsatellites in Genome Data: Variance in Definitions and Bioinformatic Approaches Cause Systematic Bias

  2008cited by this paper
• Limnoecology: The Ecology of Lakes and Streams

  2008cited by this paper
• The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex

  2008cited by this paper
• Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins

  2007cited by this paper
• Detecting microsatellites within genomes: significant variation among algorithms

  2007cited by this paper
• Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin

  2007influential reference
• UgMicroSatdb: database for mining microsatellites from unigenes

  2007cited by this paper
• Mining microsatellites in eukaryotic genomes.

  2007cited by this paper
• Divergent microsatellite evolution in the human and chimpanzee lineages

  2007cited by this paper
• Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies

  2007cited by this paper
• The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin

  2007influential reference
• Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi

  2006cited by this paper
• The rise, fall and renaissance of microsatellites in eukaryotic genomes.

  2006cited by this paper
• Insights into social insects from the genome of the honeybee Apis mellifera

  2006cited by this paper
• Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes

  2006influential reference
• TRDB—The Tandem Repeats Database

  2006cited by this paper
• Insights into social insects from the genome of the honeybee Apis mellifera

  2006cited by this paper
• Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites

  2006cited by this paper
• Erratum: Insights into social insects from the genome of the honeybee Apis mellifera

  2006cited by this paper
• A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics.

  2006cited by this paper
• Simple sequence repeats as advantageous mutators in evolution.

  2006influential reference
• Intragenic tandem repeats generate functional variability

  2005cited by this paper
• Sequence turnover and tandem repeats in cis-regulatory modules in drosophila.

  2005cited by this paper
• Survey of simple sequence repeats in completed fungal genomes.

  2005influential reference
• TRbase: a database relating tandem repeats to disease genes for the human genome

  2005cited by this paper
• Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

  2005cited by this paper
• The evolutionary dynamics of alpha-satellite.

  2005cited by this paper
• Microsatellites within genes: structure, function, and evolution.

  2004cited by this paper
• Functional microsatellite polymorphism associated with divergent social structure in vole species.

  2004cited by this paper
• Short tandem repeats are associated with diverse mRNAs encoding membrane-targeted proteins.

  2004cited by this paper
• Molecular origins of rapid and continuous morphological evolution

  2004cited by this paper
• Evolutionary theory and processes : modern horizons : papers in honour of Eviatar Nevo

  2004cited by this paper
• Microsatellites: simple sequences with complex evolution

  2004cited by this paper
• A Microsatellite-Based Linkage Map of the Honeybee, Apis mellifera L.

  2004cited by this paper
• SilkSatDb: a microsatellite database of the silkworm, Bombyx mori

  2004cited by this paper
• Five hundred and twenty-eight microsatellite markers for ecological genomic investigations using Daphnia

  2004cited by this paper
• Long perfect dinucleotide repeats are typical of vertebrates, show motif preferences and size convergence.

  2004cited by this paper
• Tuning Function of Tandemly Repeating Sequences: A Molecular Device for Fast Adaptation

  2004cited by this paper
• Transcribed short tandem repeats occur in couples with strongly preferred registers.

  2003cited by this paper
• Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions

  2003influential reference
• Development, characterisation, inheritance, and cross-species utility of American lobster (Homarus americanus) microsatellite and mtDNA PCR-RFLP markers.

  2003cited by this paper
• Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species.

  2003cited by this paper
• MICdb: database of prokaryotic microsatellites

  2003cited by this paper
• Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes

  2002cited by this paper
• Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

  2002cited by this paper
• Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review

  2002cited by this paper
• Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions.

  2002cited by this paper
• Microsatellite evolution inferred from human– chimpanzee genomic sequence alignments

  2002cited by this paper
• Differential distribution of simple sequence repeats in eukaryotic genome sequences.

  2001influential reference
• Repeat polymorphisms within gene regions: phenotypic and evolutionary implications.

  2000cited by this paper
• Microsatellites in different eukaryotic genomes: survey and analysis.

  2000influential reference
• Minisatellites: mutability and genome architecture.

  2000cited by this paper
• Evolutionary dynamics of microsatellite DNA

  2000cited by this paper
• The genome sequence of Drosophila melanogaster.

  2000cited by this paper
• Selection against frameshift mutations limits microsatellite expansion in coding DNA.

  2000cited by this paper
• Tandem repeats finder: a program to analyze DNA sequences.

  1999influential reference
• Microsatellites: Evolution and Applications

  1999cited by this paper
• Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations.

  1998cited by this paper
• Launching microsatellites: a review of mutation processes and methods of phylogenetic interference.

  1997cited by this paper
• Big, bad minisatellites

  1997cited by this paper
• Simple sequence repeats as a source of quantitative genetic variation.

  1997cited by this paper
• A comprehensive genetic map of the human genome based on 5,264 microsatellites

  1996cited by this paper
• Characterization of honeybee (Apis mellifera L.) chromosomes using repetitive DNA probes and fluorescence in situ hybridization.

  1995cited by this paper
• Microsatellite evolution — evidence for directionality and variation in rate between species

  1995cited by this paper
• Simple repetitive DNA sequences from primates: Compilation and analysis

  1995cited by this paper
• Microsatellite analysis of population structure in Canadian polar bears

  1995cited by this paper
• Characterization of (GT)n and (CT)n microsatellites in two insect species: Apis mellifera and Bombus terrestris.

  1993cited by this paper
• A second-generation linkage map of the human genome

  1992cited by this paper
• Repeat unit sequence variation in minisatellites: a novel source of DNA polymorphism for studying variation and mutation by single molecule analysis.

  1990cited by this paper
• Cryptic simplicity in DNA is a major source of genetic variation

  1986cited by this paper
• Hypervariable ‘minisatellite’ regions in human DNA

  1985cited by this paper
• Simple sequences are ubiquitous repetitive components of eukaryotic genomes.

  1984cited by this paper

• Chloroplast Genome Diversity and Marker Potentials of Diverse Ensete ventricosum Accessions

  2025cites this paper
• Phase variation in Mannheimia haemolytica challenges the static genome paradigm

  2025cites this paper
• In silico EST-SSR Identification and Development through EST Sequences from Metroxylon sagu Rottb. for Genetic Diversity Analysis

  2024influential citation
• Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus

  2024cites this paper
• WebSTR: a population-wide database of short tandem repeat variation in humans.

  2023cites this paper
• Short tandem repeat mutations regulate gene expression in colorectal cancer

  2023cites this paper
• A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)

  2023cites this paper
• Transcriptional Analysis of Microsatellites in Velvetbean Caterpillar Anticarsia gemmatalis Hübner, 1818

  2023cites this paper
• Teleost genomic repeat landscapes in light of diversification rates and ecology

  2023influential citation
• Exploring repeats in rice genomes: Identification, Characterization and its Applications

  2022cites this paper
• Structural Characterization and Comparative Analyses of the Chloroplast Genome of Eastern Asian Species Cardamine occulta (Asian C. flexuosa With.) and Other Cardamine Species.

  2022cites this paper
• Microsatellite Marker Mining Using PCR-Based Isolation of Microsatellite Arrays (PIMA) Method on Blue-Spotted Mudskipper, Boleophthalmus Boddarti

  2022cites this paper
• Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae

  2022cites this paper
• Benchmarking tools for DNA repeat identification in diverse genomes

  2021cites this paper
• Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics

  2021cites this paper
• Comparative Genome-Wide Characterization of Microsatellites in Candida albicans and Candida dubliniensis Leading to the Development of Species-Specific Marker

  2021cites this paper
• Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing.

  2021cites this paper
• Comprehensive identification and characterization of simple sequence repeats based on the whole-genome sequences of 14 forest and fruit trees

  2021cites this paper
• Intracellular gene transfer events restricted to the genus Convallaria within the Asparagaceae family: Possible mechanisms and potential as genetic markers for biographical studies.

  2021cites this paper
• The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

  2021cites this paper
• Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga.

  2020cites this paper
• Comparative analysis of whole chloroplast genomes of Ligusticum sinense and L. jeholense, Umbelliferae

  2020cites this paper
• Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

  2020cites this paper
• The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

  2020cites this paper
• Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

  2020cites this paper
• Comparison of microsatellite distribution patterns in twenty-nine beetle genomes.

  2020cites this paper
• Genomewide analysis of microsatellite markers based on sequenced database in two anuran species

  2020cites this paper
• Comparative chloroplast genomics of the genus Taxodium

  2020cites this paper
• Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb.

  2019cites this paper
• Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend

  2019cites this paper
• Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

  2019cites this paper
• A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats

  2019cites this paper
• Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection1

  2019cites this paper
• Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae

  2019cites this paper
• The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

  2019cites this paper
• Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes

  2018cites this paper
• Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

  2018influential citation
• Satellite DNA evolution: old ideas, new approaches.

  2018cites this paper
• In silico identification and characterization of stress and virulence associated repeats in Salmonella.

  2018cites this paper
• A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae)

  2018cites this paper
• A novel quantitative real-time PCR diagnostic assay for seal heartworm (Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal (Halichoerus grypus)

  2018cites this paper
• Targeted gene disruption by use of CRISPR/Cas9 ribonucleoprotein complexes in the water flea Daphnia pulex

  2018cites this paper
• Genomic architecture of codfishes featured by expansions of innate immune genes and short tandem repeats

  2017cites this paper
• Analysis of somatic microsatellite indels identifies driver events in human tumors

  2017cites this paper
• In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis

  2017cites this paper
• Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects

  2017cites this paper
• Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

  2017cites this paper
• Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas

  2017cites this paper
• Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species

  2017cites this paper
• De novo assembly and comparative genomics of teleosts

  2017cites this paper
• An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

  2016influential citation
• Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

  2016cites this paper
• The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

  2016cites this paper
• Distribution and population structure of the anther smut Microbotryum silenes‐acaulis parasitizing an arctic–alpine plant

  2016influential citation
• Parallel consideration of SSRs and differentially expressed genes under abiotic stress for targeted development of functional markers in almond and related Prunus species

  2016cites this paper
• Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii.

  2016cites this paper
• Development of 12 Microsatellite Markers in Dorcus titanus castanicolor (Motschulsky, 1861) (Lucanidae, Coleoptera) from Korea Using Next-Generation Sequencing

  2016cites this paper
• Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)

  2016cites this paper
• Simple sequence repeats in bryophyte mitochondrial genomes

  2016cites this paper
• Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island Based on Chloroplast Genome Sequencing

  2016cites this paper
• Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island, Sea of East Japan, Based on Chloroplast Genome Sequencing.

  2016cites this paper
• Hybrid de novo tandem repeat detection using short and long reads

  2015cites this paper
• Epigenetic variability in the facultative human pathogen "Neisseria meningitidis"

  2015cites this paper
• Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics

  2015cites this paper
• Evolution Analysis of Simple Sequence Repeats in Plant Genome

  2015cites this paper
• A Draft De Novo Genome Assembly and Mitochondrial Population Genomics for the Northern Bobwhite (Colinus Virginianus)

  2015cites this paper
• Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution

  2015cites this paper
• Genome-wide analysis of the associations between polyadenylation sites and repeated sequences in Arabidopsis thaliana

  2015cites this paper
• Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective

  2015cites this paper
• Pattern discovery for microsatellite genome analysis

  2014cites this paper
• Genome-Wide Analysis of Simple Sequence Repeats in Marine Animals—a Comparative Approach

  2014influential citation
• Buying in to bioinformatics: an introduction to commercial sequence analysis software

  2014cites this paper
• Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

  2014cites this paper
• A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

  2014cites this paper
• Characterization of microsatellite loci and repeat density in the gooseneck barnacle, Pollicipes elegans, using next generation sequencing.

  2014cites this paper
• Abundance, arrangement, and function of sequence motifs in the chicken promoters

  2014cites this paper
• The tiger genome and comparative analysis with lion and snow leopard genomes

  2013cites this paper
• Large tandem repeats make up the chromosome bar code: a hypothesis.

  2013cites this paper
• A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

  2013cites this paper
• Genome-Wide Analysis of Tandem Repeats in Plants and Green Algae

  2013influential citation
• Patterns of Evolutionary Conservation of Microsatellites (SSRs) Suggest a Faster Rate of Genome Evolution in Hymenoptera Than in Diptera

  2013cites this paper
• Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome

  2013cites this paper
• Locating tandem repeats in weighted sequences in proteins

  2013cites this paper
• Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

  2012cites this paper
• CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis

  2012cites this paper
• The limitations of draft assemblies for understanding prokaryotic adaptation and evolution.

  2012cites this paper
• PeanutDB: an integrated bioinformatics web portal for Arachis hypogaea transcriptomics

  2012cites this paper
• Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

  2012influential citation
• Coevolution between simple sequence repeats (SSRs) and virus genome size

  2012cites this paper
• PeanutDB: an integrated bioinformatics web portal for

  2012cites this paper
• Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus

  2011cites this paper
• Tandemly repeated DNA families in the mouse genome

  2011cites this paper
• The Ecoresponsive Genome of Daphnia pulex

  2011cites this paper
• Bioinformatic Survey of Haliotis midae Microsatellites Reveals a Non-Random Distribution of Repeat Motifs

  2011cites this paper
• Analysing intraspecific genetic variation: A practical guide using mitochondrial DNA and microsatellites

  2011cites this paper