ArticleBMC genomics2010
Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 107 citations in OpenAlex.
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- Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing.Methods in molecular biology (Clifton, N.J.) · 2021Review
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- Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny.BMC plant biology · 2020Article
- Comparative chloroplast genomics of the genus Taxodium.BMC genomics · 2020Article
- Genomewide analysis of microsatellite markers based on sequenced database in two anuran species.Journal of genetics · 2020Article
- A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats.Scientific reports · 2019Article
- Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.Nucleic acids research · 2019Review
- Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection.Plant physiology · 2019Article
- Plastid genome and composition analysis of two medical ferns:Chinese medicine · 2019Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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