Mining microsatellites in eukaryotic genomes.

During recent decades, microsatellites have become the most popular source of genetic markers. More recently, the availability of enormous sequence data for a large number of eukaryotic genomes has accelerated research aimed at understanding the origin and functions of microsatellites and searching for new applications. This review presents recent developments of in silico mining of microsatellites to reveal various facets of the distribution and dynamics of microsatellites in eukaryotic genomes. Two aspects of microsatellite search strategies--using a suitable search tool and accessing a relevant microsatellite database--have been explored. Judicious microsatellite mining not only helps in addressing biological questions but also facilitates better exploitation of microsatellites for diverse applications.

[1]  Margaret Staton,et al.  CMD: a Cotton Microsatellite Database resource for Gossypium genomics , 2006, BMC Genomics.

[2]  Jianxin Ma,et al.  Rapid recent growth and divergence of rice nuclear genomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[3]  P. Fisch,et al.  Frequent genomic alterations in epithelium measured by microsatellite instability following allogeneic hematopoietic cell transplantation in humans. , 2005, Blood.

[4]  Gary Benson,et al.  TRDB—The Tandem Repeats Database , 2006, Nucleic Acids Res..

[5]  A. Grover,et al.  Biased distribution of microsatellite motifs in the rice genome , 2007, Molecular Genetics and Genomics.

[6]  Hampapathalu A. Nagarajaram,et al.  Genome analysis IMEx : Imperfect Microsatellite Extractor , 2007 .

[7]  R. Guyomard,et al.  A Type I and Type II microsatellite linkage map of Rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms , 2006, BMC Genomics.

[8]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[9]  E. Nevo,et al.  Microsatellites within genes: structure, function, and evolution. , 2004, Molecular biology and evolution.

[10]  D. Choi,et al.  Exploitation of pepper EST–SSRs and an SSR-based linkage map , 2006, Theoretical and Applied Genetics.

[11]  S. Rensing,et al.  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, BMC Plant Biology.

[12]  B. Hohn,et al.  Extremely complex pattern of microsatellite mutation in the germline of wheat exposed to the post-Chernobyl radioactive contamination. , 2003, Mutation research.

[13]  H. Ellegren,et al.  Microsatellite evolution inferred from human– chimpanzee genomic sequence alignments , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  G. Gutman,et al.  Slipped-strand mispairing: a major mechanism for DNA sequence evolution. , 1987, Molecular biology and evolution.

[15]  C. Farber,et al.  Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. , 2003, Animal genetics.

[16]  Jerilyn A. Walker,et al.  SVA elements: a hominid-specific retroposon family. , 2005, Journal of molecular biology.

[17]  B. Gandon,et al.  Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) , 2004, Theoretical and Applied Genetics.

[18]  Eric Rivals,et al.  Detecting microsatellites within genomes: significant variation among algorithms , 2007, BMC Bioinformatics.

[19]  R. Durrett,et al.  Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. , 2001, Genetics.

[20]  Akito Taneda Adplot: detection and visualization of repetitive patterns in complete genomes , 2004, Bioinform..

[21]  Atul Grover,et al.  Microsatellite Motifs with Moderate GC Content Are Clustered Around Genes on Arabidopsis thaliana Chromosome 2 , 2007, Silico Biol..

[22]  Robert Kofler,et al.  SciRoKo: a new tool for whole genome microsatellite search and investigation , 2007, Bioinform..

[23]  M. Bilgen,et al.  Exact tandem repeats analyzer (E-TRA): A new program for DNA sequence mining , 2005, Journal of Genetics.

[24]  C. Farber,et al.  Identification of putative homology between horse microsatellite flanking sequences and cross-species ESTs, mRNAs and genomic sequences. , 2004, Animal genetics.

[25]  Christian Schlötterer,et al.  The evolution of molecular markers — just a matter of fashion? , 2004, Nature Reviews Genetics.

[26]  J. Stoye,et al.  REPuter: the manifold applications of repeat analysis on a genomic scale. , 2001, Nucleic acids research.

[27]  Ju-Kyung Yu,et al.  Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley , 2005, BMC Genomics.

[28]  C. Jones,et al.  A high incidence of clustered microsatellite mutations revealed by parent-offspring analysis in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata) , 2005, Genetica.

[29]  B. Faircloth,et al.  msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design , 2008, Molecular ecology resources.

[30]  H. Korpelainen,et al.  Microsatellite marker identification using genome screening and restriction-ligation. , 2007, BioTechniques.

[31]  Atul Grover,et al.  EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes , 2007, BMC Genomics.

[32]  R. Varshney,et al.  Organization of retrotransposons and microsatellites in cereal genomes , 2004 .

[33]  V. Poncet,et al.  SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus , 2006, Molecular Genetics and Genomics.

[34]  Eric Rivals,et al.  STAR: an algorithm to Search for Tandem Approximate Repeats , 2004, Bioinform..

[35]  S. Restrepo,et al.  Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus , 2006, BMC Genomics.

[36]  R. Sibly,et al.  Likelihood-based estimation of microsatellite mutation rates. , 2003, Genetics.

[37]  Vineet K. Sharma,et al.  (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length , 2005, BMC Genomics.

[38]  Buddhaditta Bose,et al.  SilkSatDb: a microsatellite database of the silkworm, Bombyx mori , 2004, Nucleic Acids Res..

[39]  L. Lipovich,et al.  Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. , 2001, Genome research.

[40]  K. Weising DNA fingerprinting in plants: principles, methods, and applications , 2005 .

[41]  Derrick G. Kourie,et al.  FireµSat: An algorithm to detect microsatellites in DNA , 2006, Stringology.

[42]  Gregory Kucherov,et al.  mreps: efficient and flexible detection of tandem repeats in DNA , 2003, Nucleic Acids Res..

[43]  Christian Schlötterer,et al.  Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. , 2003, Genome research.

[44]  Hampapathalu A. Nagarajaram,et al.  MICdb: database of prokaryotic microsatellites , 2003, Nucleic Acids Res..

[45]  Kenneth A. Marx,et al.  Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA , 2003, BMC Bioinformatics.

[46]  MicrosatDesign is a pipeline for transforming sequencer trace files into DNA markers , 2005 .

[47]  Gajendra P. S. Raghava,et al.  Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation , 2004, Bioinform..

[48]  Mei Peng,et al.  The direction of microsatellite mutations is dependent upon allele length , 2000, Nature Genetics.

[49]  Young A. Choi,et al.  Mining and characterizing microsatellites from citrus ESTs , 2006, Theoretical and Applied Genetics.

[50]  H. Ellegren Microsatellites: simple sequences with complex evolution , 2004, Nature Reviews Genetics.

[51]  B. Jayashree,et al.  A Database of Simple Sequence Repeats from Cereal and Legume Expressed Sequence Tags Mined in silico: Survey and Evaluation , 2006, Silico Biol..

[52]  Alan M. Durham,et al.  TRAP: automated classification, quantification and annotation of tandemly repeated sequences , 2006, Bioinform..

[53]  Asim Azfer,et al.  DNA trinucleotide repeat expansion in neuropsychiatric patients. , 2003, Medical science monitor : international medical journal of experimental and clinical research.

[54]  Kexuan Tang,et al.  Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana , 2004, Bioinform..

[55]  Hans Ellegren,et al.  Heterogeneous mutation processes in human microsatellite DNA sequences , 2000, Nature Genetics.

[56]  T. Mohapatra,et al.  Unigene derived microsatellite markers for the cereal genomes , 2006, Theoretical and Applied Genetics.

[57]  Guang R. Gao,et al.  TROLL-Tandem Repeat Occurrence Locator , 2002, Bioinform..

[58]  Filippo Aluffi-Pentini,et al.  STRING: finding tandem repeats in DNA sequences , 2003, Bioinform..

[59]  Buddhaditta Bose,et al.  MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences. , 2003, Applied bioinformatics.

[60]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[61]  Chi-Ren Shyu,et al.  ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval , 2004, Nucleic Acids Res..

[62]  J. Doebley,et al.  An Analysis of Genetic Diversity Across the Maize Genome Using Microsatellites , 2005, Genetics.

[63]  C. Schlötterer,et al.  Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome. , 1999, Molecular biology and evolution.