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Volumn 729, Issue , 2011, Pages 225-246

SNP Discovery by Transcriptome Pyrosequencing

Author keywords

Computational biology; Maize; Next generation sequencing; Pyrosequencing; SNP; Whole genome SNP discovery

Indexed keywords

PLANT DNA;

EID: 79958248844     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-065-2_15     Document Type: Chapter
Times cited : (21)

References (82)
  • 1
    • 0035010640 scopus 로고    scopus 로고
    • Automation in genotyping of single nucleotide polymorphisms
    • Gut, I. G. (2001) Automation in genotyping of single nucleotide polymorphisms. Hum. Mutat. 17, 475–492.
    • (2001) Hum. Mutat. , vol.17 , pp. 475-492
    • Gut, I.G.1
  • 2
    • 0035776497 scopus 로고    scopus 로고
    • Methods for genotyping single nucleotide polymorphisms
    • Kwok, P. Y. (2001) Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2, 235–258.
    • (2001) Annu. Rev. Genomics Hum. Genet. , vol.2 , pp. 235-258
    • Kwok, P.Y.1
  • 3
    • 0034436178 scopus 로고    scopus 로고
    • Automated mass spectrometry: A revolutionary technology for clinical diagnostics
    • Leushner, J. and Chiu, N. H. (2000) Automated mass spectrometry: a revolutionary technology for clinical diagnostics. Mol. Diagn. 5, 341–348.
    • (2000) Mol. Diagn. , vol.5 , pp. 341-348
    • Leushner, J.1    Chiu, N.H.2
  • 4
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • Consortium, T. I. H. (2003) The International HapMap Project. Nature 426, 789–796.
    • (2003) Nature , vol.426 , pp. 789-796
    • Consortium, T.I.H.1
  • 5
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • Consortium, T. I. H. (2005) A haplotype map of the human genome. Nature 437, 1299–1320.
    • (2005) Nature , vol.437 , pp. 1299-1320
    • Consortium, T.I.H.1
  • 6
    • 0037623912 scopus 로고    scopus 로고
    • Cis-acting variation in the expression of a high proportion of genes in human brain
    • Bray, N. J., Buckland, P. R., Owen, M. J., and O’Donovan, M. C. (2003) Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113, 149–153.
    • (2003) Hum. Genet. , vol.113 , pp. 149-153
    • Bray, N.J.1    Buckland, P.R.2    Owen, M.J.3    O’Donovan, M.C.4
  • 10
    • 33747866029 scopus 로고    scopus 로고
    • Cistranscriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid
    • Stupar, R. M. and Springer, N. M. (2006) Cistranscriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173, 2199–2210.
    • (2006) Genetics , vol.173 , pp. 2199-2210
    • Stupar, R.M.1    Springer, N.M.2
  • 13
    • 4644353880 scopus 로고    scopus 로고
    • An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments
    • Feltus, F. A., Wan, J., Schulze, S. R., Estill, J. C., Jiang, N., and Paterson, A. H. (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14, 1812–1819.
    • (2004) Genome Res , vol.14 , pp. 1812-1819
    • Feltus, F.A.1    Wan, J.2    Schulze, S.R.3    Estill, J.C.4    Jiang, N.5    Paterson, A.H.6
  • 15
    • 33344469072 scopus 로고    scopus 로고
    • A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement
    • Yamasaki, M., Tenaillon, M. I., Bi, I. V., Schroeder, S. G., Sanchez-Villeda, H., Doebley, J. F., Gaut, B. S., and McMullen, M. D. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17, 2859–2872.
    • (2005) Plant Cell , vol.17 , pp. 2859-2872
    • Yamasaki, M.1    Tenaillon, M.I.2    Bi, I.V.3    Schroeder, S.G.4    Sanchez-Villeda, H.5    Doebley, J.F.6    Gaut, B.S.7    McMullen, M.D.8
  • 19
    • 0036306905 scopus 로고    scopus 로고
    • Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.)
    • Kota, R., Varshney, R. K., Thiel, T., Dehmer, K. J., and Graner, A. (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135, 145–151.
    • (2001) Hereditas , vol.135 , pp. 145-151
    • Kota, R.1    Varshney, R.K.2    Thiel, T.3    Dehmer, K.J.4    Graner, A.5
  • 20
    • 16244399810 scopus 로고    scopus 로고
    • Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz)
    • Lopez, C., Piegu, B., Cooke, R., Delseny, M., Tohme, J., and Verdier, V. (2005) Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor. Appl. Genet. 110, 425–431.
    • (2005) Theor. Appl. Genet. , vol.110 , pp. 425-431
    • Lopez, C.1    Piegu, B.2    Cooke, R.3    Delseny, M.4    Tohme, J.5    Verdier, V.6
  • 22
    • 0037986743 scopus 로고    scopus 로고
    • Mining for single nucleotide polymorphisms and insertions/ deletions in maize expressed sequence tag data
    • Batley, J., Barker, G., O’Sullivan, H., Edwards, K. J., and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/ deletions in maize expressed sequence tag data. Plant Physiol. 132, 84–91.
    • (2003) Plant Physiol , vol.132 , pp. 84-91
    • Batley, J.1    Barker, G.2    O’Sullivan, H.3    Edwards, K.J.4    Edwards, D.5
  • 23
    • 44849092474 scopus 로고    scopus 로고
    • The new paradigm of flow cell sequencing
    • Holt, R. A. and Jones, S. J. (2008) The new paradigm of flow cell sequencing. Genome Res. 18, 839–846.
    • (2008) Genome Res , vol.18 , pp. 839-846
    • Holt, R.A.1    Jones, S.J.2
  • 24
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M., Egholm, M., Altman, W. E., et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 25
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley, D. R. (2006) Whole-genome re-sequencing, Curr. Opin. Genet. Dev. 16, 545–552.
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 26
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9, 868–877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 27
    • 56149112104 scopus 로고    scopus 로고
    • Wholegenome sequencing and assembly with highthroughput, short-read technologies
    • Sundquist, A., Ronaghi, M., Tang, H., Pevzner, P., and Batzoglou, S. (2007) Wholegenome sequencing and assembly with highthroughput, short-read technologies. PLoS One 2, e484.
    • (2007) Plos One , vol.2
    • Sundquist, A.1    Ronaghi, M.2    Tang, H.3    Pevzner, P.4    Batzoglou, S.5
  • 28
    • 38749091304 scopus 로고    scopus 로고
    • Pyrobayes: An improved base caller for SNP discovery in pyrosequences
    • Quinlan, A. R., Stewart, D. A., Stromberg, M. P., and Marth, G. T. (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat. Methods 5, 179–181.
    • (2008) Nat. Methods , vol.5 , pp. 179-181
    • Quinlan, A.R.1    Stewart, D.A.2    Stromberg, M.P.3    Marth, G.T.4
  • 29
  • 30
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 31
    • 33746605947 scopus 로고    scopus 로고
    • A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes
    • Goldberg, S. M., Johnson, J., Busam, D., et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl Acad. Sci. USA 103, 11240–11245.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 11240-11245
    • Goldberg, S.M.1    Johnson, J.2    Busam, D.3
  • 35
    • 33947145569 scopus 로고    scopus 로고
    • New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis
    • Smith, M. G., Gianoulis, T. A., Pukatzki, S., Mekalanos, J. J., Ornston, L. N., Gerstein, M., and Snyder, M. (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 21, 601–614.
    • (2007) Genes Dev , vol.21 , pp. 601-614
    • Smith, M.G.1    Gianoulis, T.A.2    Pukatzki, S.3    Mekalanos, J.J.4    Ornston, L.N.5    Gerstein, M.6    Snyder, M.7
  • 36
    • 33847307402 scopus 로고    scopus 로고
    • Assembling millions of short DNA sequences using SSAKE
    • Warren, R. L., Sutton, G. G., Jones, S. J., and Holt, R. A. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23, 500–501.
    • (2007) Bioinformatics , vol.23 , pp. 500-501
    • Warren, R.L.1    Sutton, G.G.2    Jones, S.J.3    Holt, R.A.4
  • 38
    • 35948929094 scopus 로고    scopus 로고
    • SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
    • Dohm, J. C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17, 1697–1706.
    • (2007) Genome Res , vol.17 , pp. 1697-1706
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 39
    • 33745279055 scopus 로고    scopus 로고
    • Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning
    • Henderson, I. R., Zhang, X., Lu, C., Johnson, L., Meyers, B. C., Green, P. J., and Jacobsen, S. E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 38, 721–725.
    • (2006) Nat. Genet. , vol.38 , pp. 721-725
    • Henderson, I.R.1    Zhang, X.2    Lu, C.3    Johnson, L.4    Meyers, B.C.5    Green, P.J.6    Jacobsen, S.E.7
  • 41
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 43
    • 40749143164 scopus 로고    scopus 로고
    • Transcript profiling by 3¢-untranslated region sequencing resolves expression of gene families
    • Eveland, A. L., McCarty, D. R., and Koch, K. E. (2008) Transcript profiling by 3¢-untranslated region sequencing resolves expression of gene families. Plant Physiol. 146, 32–44.
    • (2008) Plant Physiol , vol.146 , pp. 32-44
    • Eveland, A.L.1    McCarty, D.R.2    Koch, K.E.3
  • 44
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson, D. S., Mortazavi, A., Myers, R. M., and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 47
    • 77950946551 scopus 로고    scopus 로고
    • Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol
    • Buggs, R. J. A., Chamala, S., Wu, W., Gao, L., May, G. D., Schnable, P. S., Soltis, D. E., Soltis, P. S., and Barbazuk, W. B. (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol. Ecol. 19(S1), 132–146.
    • (2010) Ecol , vol.19 , pp. 132-146
    • Buggs, R.J.A.1    Chamala, S.2    Wu, W.3    Gao, L.4    May, G.D.5    Schnable, P.S.6    Soltis, D.E.7    Soltis, P.S.8    Barbazuk, W.B.9
  • 48
    • 33845984917 scopus 로고    scopus 로고
    • Gene discovery and annotation using LCM-454 transcriptome sequencing
    • Emrich, S. J., Barbazuk, W. B., Li, L., and Schnable, P. S. (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17, 69–73.
    • (2007) Genome Res , vol.17 , pp. 69-73
    • Emrich, S.J.1    Barbazuk, W.B.2    Li, L.3    Schnable, P.S.4
  • 52
    • 50649122770 scopus 로고    scopus 로고
    • EagleView: A genome assembly viewer for next-generation sequencing technologies
    • Huang, W. and Marth, G. (2008) EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 18, 1538–1543
    • (2008) Genome Res , vol.18 , pp. 1538-1543
    • Huang, W.1    Marth, G.2
  • 53
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202.
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 55
    • 0030872838 scopus 로고    scopus 로고
    • PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
    • Nickerson, D. A., Tobe, V. O., and Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745–2751.
    • (1997) Nucleic Acids Res , vol.25 , pp. 2745-2751
    • Nickerson, D.A.1    Tobe, V.O.2    Taylor, S.L.3
  • 56
    • 25444532272 scopus 로고    scopus 로고
    • A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
    • Wang, J. and Huang, X. (2005) A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. BMC Bioinform. 6, 220.
    • (2005) BMC Bioinform , vol.6
    • Wang, J.1    Huang, X.2
  • 59
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable, P. S., Ware, D., Fulton, R. S., et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3
  • 60
    • 24744442994 scopus 로고    scopus 로고
    • Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes
    • Fu, Y., Emrich, S. J., Guo, L., Wen, T. J., Ashlock, D. A., Aluru, S., and Schnable, P. S. (2005) Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl Acad. Sci. USA 102, 12282–12287.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 12282-12287
    • Fu, Y.1    Emrich, S.J.2    Guo, L.3    Wen, T.J.4    Ashlock, D.A.5    Aluru, S.6    Schnable, P.S.7
  • 64
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequence and analysis of the model grass Brachypodium distachyon
    • The International Brachypodium Initiative. (2010) Genome sequence and analysis of the model grass Brachypodium distachyon. Nature 463, 763–768.
    • (2010) Nature , vol.463 , pp. 763-768
  • 65
    • 0037790561 scopus 로고    scopus 로고
    • Efficient clustering of large EST data sets on parallel computers
    • Kalyanaraman, A., Aluru, S., Kothari, S., and Brendel, V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Res. 31, 2963–2974.
    • (2003) Nucleic Acids Res , vol.31 , pp. 2963-2974
    • Kalyanaraman, A.1    Aluru, S.2    Kothari, S.3    Brendel, V.4
  • 67
    • 0028485631 scopus 로고
    • Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA
    • Bennetzen, J. L., Schrick, K., Springer, P. S., Brown, W. E., and SanMiguel, P. (1994) Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565–576.
    • (1994) Genome , vol.37 , pp. 565-576
    • Bennetzen, J.L.1    Schrick, K.2    Springer, P.S.3    Brown, W.E.4    Sanmiguel, P.5
  • 70
  • 73
    • 25844507219 scopus 로고    scopus 로고
    • Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries
    • Emberton, J., Ma, J., Yuan, Y., SanMiguel, P., and Bennetzen, J. L. (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 10, 1441–1446.
    • (2005) Genome Res , Issue.10 , pp. 1441-1446
    • Emberton, J.1    Ma, J.2    Yuan, Y.3    Sanmiguel, P.4    Bennetzen, J.L.5
  • 74
    • 0016000938 scopus 로고
    • Analysis of repeating DNA sequences by reassociation
    • Britten, R. J., Graham, D. E., and Neufeld, B. R. (1974) Analysis of repeating DNA sequences by reassociation. Methods Enzymol. 29, 363–418.
    • (1974) Methods Enzymol , vol.29 , pp. 363-418
    • Britten, R.J.1    Graham, D.E.2    Neufeld, B.R.3
  • 75
    • 0036843242 scopus 로고    scopus 로고
    • Efficient capture of unique sequences from eukaryotic genomes
    • Peterson, D. G., Wessler, S. R., and Paterson, A. H. (2002) Efficient capture of unique sequences from eukaryotic genomes. Trends Genet. 18, 547–550.
    • (2002) Trends Genet , vol.18 , pp. 547-550
    • Peterson, D.G.1    Wessler, S.R.2    Paterson, A.H.3
  • 76
    • 0013152891 scopus 로고    scopus 로고
    • High-Cot sequence analysis of the maize genome
    • Yuan, Y., SanMiguel, P. J., and Bennetzen, J. L. (2003) High-Cot sequence analysis of the maize genome. Plant J. 34, 249–255.
    • (2003) Plant J , vol.34 , pp. 249-255
    • Yuan, Y.1    Sanmiguel, P.J.2    Bennetzen, J.L.3
  • 77
    • 24644437451 scopus 로고    scopus 로고
    • Reduced representation sequencing: A success in maize and a promise for other plant genomes
    • Barbazuk, W. B., Bedell, J. A., and Rabinowicz, P. D. (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27, 839–848.
    • (2005) Bioessays , vol.27 , pp. 839-848
    • Barbazuk, W.B.1    Bedell, J.A.2    Rabinowicz, P.D.3


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