메뉴 건너뛰기




Volumn 4, Issue 1, 2014, Pages 67-78

Genome-Wide analysis of tandem repeats in plants and green algae

Author keywords

Genomes; Green algae; Plants; SSR; Tandem repeats

Indexed keywords

HEXANUCLEOTIDE; NUCLEOTIDE; SPACER DNA; TRINUCLEOTIDE; UNCLASSIFIED DRUG;

EID: 84892727951     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.008524     Document Type: Article
Times cited : (51)

References (47)
  • 1
    • 50649109231 scopus 로고    scopus 로고
    • Genome-wide analyses of alternative splicing in plants: opportunities and challenges
    • Barbazuk, W. B., Y. Fu, and K. M. McGinnis, 2008 Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 18: 1381-1392.
    • (2008) Genome Res , vol.18 , pp. 1381-1392
    • Barbazuk, W.B.1    Fu, Y.2    McGinnis, K.M.3
  • 2
    • 60349124979 scopus 로고    scopus 로고
    • Mononucleotide repeats represent an important source of polymorphic microsatellite markers in Aspergillus nidulans
    • Christians, J. K., and C. A. Watt, 2009 Mononucleotide repeats represent an important source of polymorphic microsatellite markers in Aspergillus nidulans. Molecular Ecology Resources 9: 572-578.
    • (2009) Molecular Ecology Resources , vol.9 , pp. 572-578
    • Christians, J.K.1    Watt, C.A.2
  • 4
    • 0034695931 scopus 로고    scopus 로고
    • Distributions of dimeric tandem repeats in non-coding and coding DNA sequences
    • Dokholyan, N. V., S. V. Buldyrev, S. Havlin, and H. E. Stanley, 2000 Distributions of dimeric tandem repeats in non-coding and coding DNA sequences. J. Theor. Biol. 202: 273-282.
    • (2000) J. Theor. Biol , vol.202 , pp. 273-282
    • Dokholyan, N.V.1    Buldyrev, V.2    Havlin, S.3    Stanley, H.E.4
  • 5
    • 0142184516 scopus 로고    scopus 로고
    • A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription
    • Fujimori, S., T. Washio, K. Higo, Y. Ohtomo, K. Murakami et al., 2003 A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett. 554: 17-22.
    • (2003) FEBS Lett , vol.554 , pp. 17-22
    • Fujimori, S.1    Washio, T.2    Higo, K.3    Ohtomo, Y.4    Murakami, K.5
  • 6
    • 84865067382 scopus 로고    scopus 로고
    • Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences
    • Gemayel, R., J. Cho, S. Boeynaems, and K. J. Verstrepen, 2012 Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences. Genes 3: 461-480.
    • (2012) Genes , vol.3 , pp. 461-480
    • Gemayel, R.1    Cho, J.2    Boeynaems, S.3    Verstrepen, K.J.4
  • 7
    • 78149432728 scopus 로고    scopus 로고
    • Variable tandem repeats accelerate evolution of coding and regulatory sequences
    • Gemayel, R., M. D. Vinces, M. Legendre, and K. J. Verstrepen, 2010 Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu. Rev. Genet. 44: 445-477.
    • (2010) Annu. Rev. Genet , vol.44 , pp. 445-477
    • Gemayel, R.1    Vinces, M.D.2    Legendre, M.3    Verstrepen, K.J.4
  • 8
    • 66449106867 scopus 로고    scopus 로고
    • Gene regulation by sense-antisense overlap of polyadenylation signals
    • Gu, R., Z. Zhang, J. N. DeCerbo, and G. G. Carmichael, 2009 Gene regulation by sense-antisense overlap of polyadenylation signals. RNA 15: 1154-1163.
    • (2009) RNA , vol.15 , pp. 1154-1163
    • Gu, R.1    Zhang, Z.2    DeCerbo, J.N.3    Carmichael, G.G.4
  • 9
    • 0028952245 scopus 로고
    • Simple repetitive DNA sequences from primates: compilation and analysis
    • Jurka, J., and C. Pethiyagoda, 1995 Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 40: 120-126.
    • (1995) J. Mol. Evol , vol.40 , pp. 120-126
    • Jurka, J.1    Pethiyagoda, C.2
  • 11
    • 84892703358 scopus 로고    scopus 로고
    • Genome-wide computational analysis of Chlamydomonas reinhardtii promoters
    • OhioLINK ETD Center. Available at:
    • Kokulapalan, W., 2011 Genome-wide computational analysis of Chlamydomonas reinhardtii promoters. OhioLINK ETD Center. Available at: https://etd.ohiolink.edu/ap:10:0::NO:10:P10_ETD_SUBID:57668.
    • (2011)
    • Kokulapalan, W.1
  • 12
    • 82355186181 scopus 로고    scopus 로고
    • In silico analysis of SSRs in mitochondrial genomes of plants
    • Kuntal, H., and V. Sharma, 2011 In silico analysis of SSRs in mitochondrial genomes of plants. OMICS 15: 783-789.
    • (2011) OMICS , vol.15 , pp. 783-789
    • Kuntal, H.1    Sharma, V.2
  • 13
    • 33745033519 scopus 로고    scopus 로고
    • Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes
    • Lawson, M. J., and L. Zhang, 2006 Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol. 7: R14.
    • (2006) Genome Biol , vol.7
    • Lawson, M.J.1    Zhang, L.2
  • 14
    • 38849170546 scopus 로고    scopus 로고
    • Sequence-based estimation of minisatellite and microsatellite repeat variability
    • Legendre, M., N. Pochet, T. Pak, and K. J. Verstrepen, 2007 Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. 17: 1787-1796.
    • (2007) Genome Res , vol.17 , pp. 1787-1796
    • Legendre, M.1    Pochet, N.2    Pak, T.3    Verstrepen, K.J.4
  • 15
    • 15244344323 scopus 로고    scopus 로고
    • Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes
    • Li, B., Q. Xia, C. Lu, Z. Zhou, and Z. Xiang, 2004 Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes. Genomics Proteomics Bioinformatics 2: 24-31.
    • (2004) Genomics Proteomics Bioinformatics , vol.2 , pp. 24-31
    • Li, B.1    Xia, Q.2    Lu, C.3    Zhou, Z.4    Xiang, Z.5
  • 16
    • 0036897944 scopus 로고    scopus 로고
    • Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review
    • Li, Y.-C., A. B. Korol, T. Fahima, A. Beiles, and E. Nevo, 2002 Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11: 2453-2465.
    • (2002) Mol. Ecol , vol.11 , pp. 2453-2465
    • Li, Y.-C.1    Korol, A.B.2    Fahima, T.3    Beiles, A.4    Nevo, E.5
  • 17
    • 84859323535 scopus 로고    scopus 로고
    • Evolutionary pressures on simple sequence repeats in prokaryotic coding regions
    • Lin, W.-H., and E. Kussell, 2011 Evolutionary pressures on simple sequence repeats in prokaryotic coding regions. Nucleic Acids Res. 40: 2399-2413.
    • (2011) Nucleic Acids Res , vol.40 , pp. 2399-2413
    • Lin, W.-H.1    Kussell, E.2
  • 18
    • 14844345314 scopus 로고    scopus 로고
    • Microsatellite instability regulates transcription factor binding and gene expression
    • USA
    • Martin, P., K. Makepeace, S. A. Hill, D. W. Hood, and E. R. Moxon, 2005 Microsatellite instability regulates transcription factor binding and gene expression. Proc. Natl. Acad. Sci. USA 102: 3800-3804.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 3800-3804
    • Martin, P.1    Makepeace, K.2    Hill, S.A.3    Hood, D.W.4    Moxon, E.R.5
  • 19
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: towards a cellular code
    • Matlin, A. J., F. Clark, and C. W. J. Smith, 2005 Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6: 386-398.
    • (2005) Nat. Rev. Mol. Cell Biol , vol.6 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.J.3
  • 20
    • 77951586434 scopus 로고    scopus 로고
    • Genome-wide analysis of tandem repeats in Daphnia pulex-a comparative approach
    • Mayer, C., F. Leese, and R. Tollrian, 2010 Genome-wide analysis of tandem repeats in Daphnia pulex-a comparative approach. BMC Genomics 11: 277.
    • (2010) BMC Genomics , vol.11 , pp. 277
    • Mayer, C.1    Leese, F.2    Tollrian, R.3
  • 21
    • 84873032132 scopus 로고    scopus 로고
    • Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
    • Melters, D. P., K. R. Bradnam, H. A. Young, N. Telis, M. R. May et al., 2013 Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 14: R10.
    • (2013) Genome Biol , vol.14
    • Melters, D.P.1    Bradnam, K.R.2    Young, H.A.3    Telis, N.4    May, M.R.5
  • 22
    • 0036125393 scopus 로고    scopus 로고
    • Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations
    • Metzgar, D., L. Liu, C. Hansen, K. Dybvig, and C. Wills, 2002 Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations. Genome Res. 12: 408-413.
    • (2002) Genome Res , vol.12 , pp. 408-413
    • Metzgar, D.1    Liu, L.2    Hansen, C.3    Dybvig, K.4    Wills, C.5
  • 23
    • 0036478903 scopus 로고    scopus 로고
    • Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes
    • Morgante, M., M. Hanafey, and W. Powell, 2002 Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200.
    • (2002) Nat. Genet , vol.30 , pp. 194-200
    • Morgante, M.1    Powell, W.2
  • 24
    • 77950236892 scopus 로고    scopus 로고
    • Homopolymeric tracts represent a general regulatory mechanism in prokaryotes
    • Orsi, R. H., B. M. Bowen, and M. Wiedmann, 2010 Homopolymeric tracts represent a general regulatory mechanism in prokaryotes. BMC Genomics 11: 102.
    • (2010) BMC Genomics , vol.11 , pp. 102
    • Orsi, R.H.1    Bowen, B.M.2    Wiedmann, M.3
  • 26
    • 0036855185 scopus 로고    scopus 로고
    • Abundant raw material for cisregulatory evolution in humans
    • Rockman, M. V., and G. A. Wray, 2002 Abundant raw material for cisregulatory evolution in humans. Mol. Biol. Evol. 19: 1991-2004.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1991-2004
    • Rockman, M.V.1    Wray, G.A.2
  • 27
    • 84892711293 scopus 로고    scopus 로고
    • Mining functional microsatellites in legume unigenes
    • Roorkiwal, M., and P. C. Sharma, 2011 Mining functional microsatellites in legume unigenes. Bioinformation 7: 264-270.
    • (2011) Bioinformation , vol.7 , pp. 264-270
    • Roorkiwal, M.1    Sharma, P.C.2
  • 28
    • 42449107363 scopus 로고    scopus 로고
    • annot8r: GO, EC and KEGG annotation of EST datasets
    • Schmid, R., and M. L. Blaxter, 2008 annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics 9: 180.
    • (2008) BMC Bioinformatics , vol.9 , pp. 180
    • Schmid, R.1    Blaxter, M.L.2
  • 29
    • 35648929376 scopus 로고    scopus 로고
    • Mining microsatellites in eukaryotic genomes
    • Sharma, P. C., A. Grover, and G. Kahl, 2007 Mining microsatellites in eukaryotic genomes. Trends Biotechnol. 25: 490-498.
    • (2007) Trends Biotechnol , vol.25 , pp. 490-498
    • Sharma, P.C.1    Grover, A.2    Kahl, G.3
  • 30
    • 0025800526 scopus 로고
    • Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy
    • La Spada, A. R., E. M. Wilson, D. B. Lubahn, A. E. Harding, and K. H. Fischbeck, 1991 Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy. Nature 352: 77-79.
    • (1991) Nature , vol.352 , pp. 77-79
    • La Spada, A.R.1    Wilson, E.M.2    Lubahn, D.B.3    Harding, A.E.4    Fischbeck, K.H.5
  • 31
    • 0036366727 scopus 로고    scopus 로고
    • Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia
    • Streelman, J. T., and T. D. Kocher, 2002 Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiol. Genomics 9: 1-4.
    • (2002) Physiol. Genomics , vol.9 , pp. 1-4
    • Streelman, J.T.1    Kocher, T.D.2
  • 32
    • 0037268258 scopus 로고    scopus 로고
    • Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions
    • Subramanian, S., R. K. Mishra, and L. Singh, 2003 Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 4: R13.
    • (2003) Genome Biol , vol.4
    • Subramanian, S.1    Mishra, R.K.2    Singh, L.3
  • 33
    • 60749097197 scopus 로고    scopus 로고
    • A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana
    • Sureshkumar, S., M. Todesco, K. Schneeberger, R. Harilal, S. Balasubramanian et al., 2009 A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science 323: 1060-1063.
    • (2009) Science , vol.323 , pp. 1060-1063
    • Sureshkumar, S.1    Todesco, M.2    Schneeberger, K.3    Harilal, R.4    Balasubramanian, S.5
  • 34
    • 0021770546 scopus 로고
    • Simple sequences are ubiquitous repetitive components of eukaryotic genomes
    • Tautz, D., and M. Renz, 1984 Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 12: 4127-4138.
    • (1984) Nucleic Acids Res , vol.12 , pp. 4127-4138
    • Tautz, D.1    Renz, M.2
  • 35
    • 0033858199 scopus 로고    scopus 로고
    • Microsatellites in different eukaryotic genomes: survey and analysis
    • Tóth, G., Z. Gáspári, and J. Jurka, 2000 Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10: 967-981.
    • (2000) Genome Res , vol.10 , pp. 967-981
    • Tóth, G.1    Gáspári, Z.2    Jurka, J.3
  • 36
    • 0025905795 scopus 로고
    • Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome
    • Verkerk, A. J., M. Pieretti, J. S. Sutcliffe, Y. H. Fu, D. P. Kuhl et al., 1991 Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell 65: 905-914.
    • (1991) Cell , vol.65 , pp. 905-914
    • Verkerk, A.J.1    Pieretti, M.2    Sutcliffe, J.S.3    Fu, Y.H.4    Kuhl, D.P.5
  • 37
    • 25144494777 scopus 로고    scopus 로고
    • Intragenic tandem repeats generate functional variability
    • Verstrepen, K. J., A. Jansen, F. Lewitter, and G. R. Fink, 2005 Intragenic tandem repeats generate functional variability. Nat. Genet. 37: 986-990.
    • (2005) Nat. Genet , vol.37 , pp. 986-990
    • Verstrepen, K.J.1    Jansen, A.2    Lewitter, F.3    Fink, G.R.4
  • 38
    • 78651510415 scopus 로고    scopus 로고
    • In silico comparative analysis of SSR markers in plants
    • Victoria, F. C., L. C. da Maia, and A. de Oliveira, 2011 In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11: 15.
    • (2011) BMC Plant Biol , vol.11 , pp. 15
    • Victoria, F.C.1    da Maia, L.C.2    de Oliveira, A.3
  • 39
    • 66349113764 scopus 로고    scopus 로고
    • Unstable tandem repeats in promoters confer transcriptional evolvability
    • Vinces, M. D., M. Legendre, M. Caldara, M. Hagihara, and K. J. Verstrepen, 2009 Unstable tandem repeats in promoters confer transcriptional evolvability. Science 324: 1213-1216.
    • (2009) Science , vol.324 , pp. 1213-1216
    • Vinces, M.D.1    Legendre, M.2    Caldara, M.3    Hagihara, M.4    Verstrepen, K.J.5
  • 40
    • 33746718089 scopus 로고    scopus 로고
    • 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
    • von Stackelberg, M., S. A. Rensing, and R. Reski, 2006 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. BMC Plant Biol. 6: 9.
    • (2006) BMC Plant Biol , vol.6 , pp. 9
    • von Stackelberg, M.1    Rensing, S.A.2    Reski, R.3
  • 41
    • 33846225133 scopus 로고    scopus 로고
    • Huntington's disease
    • Walker, F. O., 2007 Huntington's disease. Lancet 369: 218-228.
    • (2007) Lancet , vol.369 , pp. 218-228
    • Walker, F.O.1
  • 42
    • 0004160359 scopus 로고    scopus 로고
    • Practical data analysis for designed experiments
    • Chapman & Hall, London, New York
    • Yandell, B. S., 1997 Practical data analysis for designed experiments, Chapman & Hall, London, New York.
    • (1997)
    • Yandell, B.S.1
  • 43
    • 2442687890 scopus 로고    scopus 로고
    • Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana
    • Zhang, L., D. Yuan, S. Yu, Z. Li, Y. Cao et al., 2004 Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20: 1081-1086.
    • (2004) Bioinformatics , vol.20 , pp. 1081-1086
    • Zhang, L.1    Yuan, D.2    Yu, S.3    Li, Z.4    Cao, Y.5
  • 44
    • 33846805782 scopus 로고    scopus 로고
    • Conservation of noncoding microsatellites in plants: implication for gene regulation
    • Zhang, L., K. Zuo, F. Zhang, Y. Cao, J. Wang et al., 2006 Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics 7: 323.
    • (2006) BMC Genomics , vol.7 , pp. 323
    • Zhang, L.1    Zuo, K.2    Zhang, F.3    Cao, Y.4    Wang, J.5
  • 45
    • 84865485469 scopus 로고    scopus 로고
    • Coevolution between simple sequence repeats (SSRs) and virus genome size
    • Zhao, X., Y. Tian, R. Yang, H. Feng, Q. Ouyang et al., 2012 Coevolution between simple sequence repeats (SSRs) and virus genome size. BMC Genomics 13: 435.
    • (2012) BMC Genomics , vol.13 , pp. 435
    • Zhao, X.1    Tian, Y.2    Yang, R.3    Feng, H.4    Ouyang, Q.5
  • 46
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    • Zheng, Q., and X.-J. Wang, 2008 GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36: W358-W363.
    • (2008) Nucleic Acids Res , vol.36
    • Zheng, Q.1    Wang, X.-J.2
  • 47
    • 84155191038 scopus 로고    scopus 로고
    • Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes
    • Zhou, Y., J. Liu, L. Han, Z.-G. Li, and Z. Zhang, 2011 Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes. BMC Genomics 12: 632.
    • (2011) BMC Genomics , vol.12 , pp. 632
    • Zhou, Y.1    Liu, J.2    Han, L.3    Li, Z.-G.4    Zhang, Z.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.