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Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach
BACKGROUND: DNA 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 s...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152781/ https://www.ncbi.nlm.nih.gov/pubmed/20433735 http://dx.doi.org/10.1186/1471-2164-11-277 |
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author | Mayer, Christoph Leese, Florian Tollrian, Ralph |
author_facet | Mayer, Christoph Leese, Florian Tollrian, Ralph |
author_sort | Mayer, Christoph |
collection | PubMed |
description | BACKGROUND: DNA 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. RESULTS: Profound 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. CONCLUSIONS: TRs 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. |
format | Online Article Text |
id | pubmed-3152781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31527812011-08-10 Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach Mayer, Christoph Leese, Florian Tollrian, Ralph BMC Genomics Research Article BACKGROUND: DNA 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. RESULTS: Profound 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. CONCLUSIONS: TRs 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. BioMed Central 2010-04-30 /pmc/articles/PMC3152781/ /pubmed/20433735 http://dx.doi.org/10.1186/1471-2164-11-277 Text en Copyright ©2010 Mayer et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Mayer, Christoph Leese, Florian Tollrian, Ralph Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title | Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title_full | Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title_fullStr | Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title_full_unstemmed | Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title_short | Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach |
title_sort | genome-wide analysis of tandem repeats in daphnia pulex - a comparative approach |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152781/ https://www.ncbi.nlm.nih.gov/pubmed/20433735 http://dx.doi.org/10.1186/1471-2164-11-277 |
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