Differential distribution of simple sequence repeats in eukaryotic genome sequences

Complete chromosome/genome sequences available from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae were analyzed for the occurrence of mono-, di-, tri-, and tetranucleotide repeats. In all of the genomes studied, dinucleotide repeat stretc...

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Bibliographic Details
Published in:Molecular biology and evolution 2001-07, Vol.18 (7), p.1161-1167
Main Authors: Katti, M V, Ranjekar, P K, Gupta, V S
Format: Article
Language:English
Subjects:
Animals
Arabidopsis thaliana
Base Sequence
Caenorhabditis elegans
Caenorhabditis elegans - genetics
Dinucleotide Repeats
DNA - genetics
DNA, Fungal - genetics
DNA, Helminth - genetics
Drosophila melanogaster
Drosophila melanogaster - genetics
Evolution, Molecular
Genome
Genome, Fungal
Genome, Human
Humans
Microsatellite Repeats
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
simple sequence repeat
Species Specificity
Trinucleotide Repeats
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Summary:Complete chromosome/genome sequences available from humans, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae were analyzed for the occurrence of mono-, di-, tri-, and tetranucleotide repeats. In all of the genomes studied, dinucleotide repeat stretches tended to be longer than other repeats. Additionally, tetranucleotide repeats in humans and trinucleotide repeats in Drosophila also seemed to be longer. Although the trends for different repeats are similar between different chromosomes within a genome, the density of repeats may vary between different chromosomes of the same species. The abundance or rarity of various di- and trinucleotide repeats in different genomes cannot be explained by nucleotide composition of a sequence or potential of repeated motifs to form alternative DNA structures. This suggests that in addition to nucleotide composition of repeat motifs, characteristic DNA replication/repair/recombination machinery might play an important role in the genesis of repeats. Moreover, analysis of complete genome coding DNA sequences of Drosophila, C. elegans, and yeast indicated that expansions of codon repeats corresponding to small hydrophilic amino acids are tolerated more, while strong selection pressures probably eliminate codon repeats encoding hydrophobic and basic amino acids. The locations and sequences of all of the repeat loci detected in genome sequences and coding DNA sequences are available at http://www.ncl-india.org/ssr and could be useful for further studies.
ISSN:0737-4038
1537-1719
DOI:10.1093/oxfordjournals.molbev.a003903