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Mar Biotechnol (NY)
2014 Oct 01;165:604-19. doi: 10.1007/s10126-014-9580-1.
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Genome-wide analysis of simple sequence repeats in marine animals-a comparative approach.
Jiang Q
,
Li Q
,
Yu H
,
Kong L
.
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Tandem simple sequence repeats (SSRs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. High mutability makes SSRs play a role in genome evolution and correspondingly show different patterns. Comparative analysis of genomic SSRs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. This study examined the abundance of genomic SSRs with repeated unit lengths of 1-6 bp in 30 marine animals including nine taxonomic groups and further compared with the land species. More than thousands of SSRs were discovered in every organism which provided a huge resource for the development of molecular markers. Thirty marine animals showed profound differences in SSR characteristics, but some group-specific trends were also found. Both similarities and differences of repeat patterns were discovered between the land and marine species. Two taxon-specific SSR types were discovered: the pentanucleotides motif AGAGG in Euteleostei and the hexanucleotide repeats of ATGTAC in Porifera and Echinodermata. Gene ontology (GO) enrichment analysis of two representative species (Amphimedon queenslandica for Porifera and Strongylocentrotus purpuratus for Echinodermata) revealed functional preference of the ATGTAC motif associated genes, and this might hint at evolutionary significance.
Bachtrog,
Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome.
1999, Pubmed
Bachtrog,
Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome.
1999,
Pubmed
Cohen,
Simple DNA sequences in homologous flanking regions near immunoglobulin VH genes: a role in gene interaction?
1982,
Pubmed
Dybvig,
A chicken repetitive DNA sequence that is highly sensitive to single-strand specific endonucleases.
1983,
Pubmed
Field,
Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces.
1998,
Pubmed
Gebhardt,
Modulation of EGFR gene transcription by secondary structures, a polymorphic repetitive sequence and mutations--a link between genetics and epigenetics.
2000,
Pubmed
Gebhardt,
Modulation of epidermal growth factor receptor gene transcription by a polymorphic dinucleotide repeat in intron 1.
1999,
Pubmed
Hancock,
Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects.
2002,
Pubmed
Hollenbeck,
Use of comparative genomics to develop EST-SSRs for red drum (Sciaenops ocellatus).
2012,
Pubmed
Jurka,
Simple repetitive DNA sequences from primates: compilation and analysis.
1995,
Pubmed
Karaoglu,
Survey of simple sequence repeats in completed fungal genomes.
2005,
Pubmed
Karlin,
Compositional biases of bacterial genomes and evolutionary implications.
1997,
Pubmed
Katti,
Differential distribution of simple sequence repeats in eukaryotic genome sequences.
2001,
Pubmed
Kofler,
SciRoKo: a new tool for whole genome microsatellite search and investigation.
2007,
Pubmed
La Rota,
Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley.
2005,
Pubmed
Lawson,
Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.
2006,
Pubmed
Li,
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review.
2002,
Pubmed
Li,
Microsatellites within genes: structure, function, and evolution.
2004,
Pubmed
Liu,
A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus).
2012,
Pubmed
Mayer,
Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach.
2010,
Pubmed
Meloni,
A tetranucleotide polymorphic microsatellite, located in the first intron of the tyrosine hydroxylase gene, acts as a transcription regulatory element in vitro.
1998,
Pubmed
Morgante,
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.
2002,
Pubmed
Moxon,
Adaptive evolution of highly mutable loci in pathogenic bacteria.
1994,
Pubmed
Müller,
Bauplan of urmetazoa: basis for genetic complexity of metazoa.
2004,
Pubmed
Pérez,
Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy.
2005,
Pubmed
Rubinsztein,
Microsatellite evolution--evidence for directionality and variation in rate between species.
1995,
Pubmed
Sarika,
In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB.
2013,
Pubmed
Schlötterer,
Evolutionary dynamics of microsatellite DNA.
2000,
Pubmed
Schug,
Low mutation rates of microsatellite loci in Drosophila melanogaster.
1997,
Pubmed
Srivastava,
The Amphimedon queenslandica genome and the evolution of animal complexity.
2010,
Pubmed
Subramanian,
Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions.
2003,
Pubmed
Suzuki,
The molecular evolution of the pif family proteins in various species of mollusks.
2013,
Pubmed
Tautz,
Cryptic simplicity in DNA is a major source of genetic variation.
1986,
Pubmed
Tóth,
Microsatellites in different eukaryotic genomes: survey and analysis.
2000,
Pubmed
Wang,
Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome.
2010,
Pubmed
Weber,
Mutation of human short tandem repeats.
1993,
Pubmed
Webster,
Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments.
2002,
Pubmed
Werner,
Site-specific location of covalent DNA-polypeptide complexes in the chicken genome.
1989,
Pubmed
Xu,
The direction of microsatellite mutations is dependent upon allele length.
2000,
Pubmed
Ye,
WEGO: a web tool for plotting GO annotations.
2006,
Pubmed
Young,
Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae.
2000,
Pubmed
van Belkum,
Short-sequence DNA repeats in prokaryotic genomes.
1998,
Pubmed
von Stackelberg,
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.
2006,
Pubmed