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Volumn 11, Issue 1, 2012, Pages 3-11

Current state-of-art of sequencing technologies for plant genomics research

Author keywords

Genomic selection; Genotyping by sequencing; Next generation sequencing technology; Plant genomics; Sequencing by synthesis; Single molecule sequencing

Indexed keywords

DNA POLYMERASE; TRANSCRIPTOME;

EID: 84863143122     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elr045     Document Type: Article
Times cited : (114)

References (46)
  • 1
    • 79958800854 scopus 로고    scopus 로고
    • Implication of next-generation sequencing on association studies
    • Siu H, Zhu Y, Jin L, et al. Implication of next-generation sequencing on association studies. BMC Genomics 2011;12: 322.
    • (2011) BMC Genomics , vol.12 , pp. 322
    • Siu, H.1    Zhu, Y.2    Jin, L.3
  • 2
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire RJ, Glaubitz JC, Sun Q, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011;6:e19379.
    • (2011) PLoS One , vol.6
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3
  • 3
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and de novo assembly of the giant panda genome
    • Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010;463: 311-17.
    • (2010) Nature , vol.463 , pp. 311-317
    • Li, R.1    Fan, W.2    Tian, G.3
  • 4
    • 77955874456 scopus 로고    scopus 로고
    • Direct sequencing of the human microbiome readily reveals community differences
    • Kuczynski J, Costello EK, Nemergut DR, et al. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol 2010;11:210.
    • (2010) Genome Biol , vol.11 , pp. 210
    • Kuczynski, J.1    Costello, E.K.2    Nemergut, D.R.3
  • 5
    • 79958805159 scopus 로고    scopus 로고
    • Statistical quantification of methylation levels by next-generation sequencing
    • Wu G, Yi N, Absher D, et al. Statistical quantification of methylation levels by next-generation sequencing. PLoS ONE 2011;6:e21034.
    • (2011) PLoS ONE , vol.6
    • Wu, G.1    Yi, N.2    Absher, D.3
  • 6
    • 80052500402 scopus 로고    scopus 로고
    • Large-scale transcriptome analysis in chickpea (Cicerarietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa
    • Hiremath PJ, Farmer A, Cannon SB, et al. Large-scale transcriptome analysis in chickpea (Cicerarietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant BiotechJ 2011;8:922-31.
    • (2011) Plant BiotechJ , vol.8 , pp. 922-931
    • Hiremath, P.J.1    Farmer, A.2    Cannon, S.B.3
  • 7
    • 71049166845 scopus 로고    scopus 로고
    • A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L)
    • Varshney RK, Hiremath PJ, Lekha PT, et al. A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMCGenomics 2009a;10:523.
    • (2009) BMCGenomics , vol.10 , pp. 523
    • Varshney, R.K.1    Hiremath, P.J.2    Lekha, P.T.3
  • 8
    • 69449099392 scopus 로고    scopus 로고
    • Comparison of next generation sequencing technologies for transcriptome characterization
    • Wall PK, Leebens-Mack J, Chanderbali AS, et al. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 2009;10: 347.
    • (2009) BMC Genomics , vol.10 , pp. 347
    • Wall, P.K.1    Leebens-Mack, J.2    Chanderbali, A.S.3
  • 11
    • 84975742565 scopus 로고    scopus 로고
    • The 1000 Genomes Project, Consortium. A map of human genome variation from population-scale, sequencing
    • The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73.
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 12
    • 0034649566 scopus 로고    scopus 로고
    • The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000;408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 13
    • 0037023349 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
    • Goff S, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002;296: 92-100.
    • (2002) Science , vol.296 , pp. 92-100
    • Goff, S.1    Ricke, D.2    Lan, T.H.3
  • 14
    • 0037023384 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    • Yu J, Hu S, Wang S, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002;296:79-92.
    • (2002) Science , vol.296 , pp. 79-92
    • Yu, J.1    Hu, S.2    Wang, S.3
  • 15
    • 58449137410 scopus 로고    scopus 로고
    • The Sorghum bicolor genome and the diversification of grasses
    • Paterson A, Bowers J, Bruggmann R, et al. The Sorghum bicolor genome and the diversification of grasses. Nature 2009;457:551-6.
    • (2009) Nature , vol.457 , pp. 551-556
    • Paterson, A.1    Bowers, J.2    Bruggmann, R.3
  • 16
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon O, Aury JM, Noel B, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007;449:463-7.
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1    Aury, J.M.2    Noel, B.3
  • 17
    • 33748760611 scopus 로고    scopus 로고
    • The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    • Tuskan G, DiFazio, Jannson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006;313:1596-1604.
    • (2006) Science , vol.313 , pp. 1596-1604
    • Tuskan, G.1    DiFazio, S.2    Jannson, S.3
  • 18
    • 74549221016 scopus 로고    scopus 로고
    • Genome sequence of the palaeopolyploid soybean
    • Schmutz J, Cannon S, Schlueter J, et al. Genome sequence of the palaeopolyploid soybean. Nature 2010; 463:178-83.
    • (2010) Nature , vol.463 , pp. 178-183
    • Schmutz, J.1    Cannon, S.2    Schlueter, J.3
  • 19
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008;26:1135-45.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 20
    • 68949186256 scopus 로고    scopus 로고
    • Next-generation sequencing technologies and their implications for crop genetics and breeding
    • Varshney RK, Nayak SN, May GD, et al. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 2009b;27:522-30.
    • (2009) Trends Biotechnol , vol.27 , pp. 522-530
    • Varshney, R.K.1    Nayak, S.N.2    May, G.D.3
  • 21
    • 69949135779 scopus 로고    scopus 로고
    • Swift: primary data analysis for the Illumina/Solexa sequencing platform
    • Whiteford N, Skelly T, Curtis C, et al. Swift: primary data analysis for the Illumina/Solexa sequencing platform. Bioinformatics 2009;25:2194-9.
    • (2009) Bioinformatics , vol.25 , pp. 2194-2199
    • Whiteford, N.1    Skelly, T.2    Curtis, C.3
  • 22
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010;1:31-46.
    • (2010) Nat Rev Genet , vol.1 , pp. 31-46
    • Metzker, M.L.1
  • 23
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second-generation sequencing
    • Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res 2010;20:1165-73.
    • (2010) Genome Res , vol.20 , pp. 1165-1173
    • Schatz, M.C.1    Delcher, A.L.2    Salzberg, S.L.3
  • 24
    • 79251632958 scopus 로고    scopus 로고
    • The genome of Theobroma cacao
    • Argout X, Salse J, Aury J-M, et al. The genome of Theobroma cacao. Nat Genet 2011;43:101-8.
    • (2011) Nat Genet , vol.43 , pp. 101-108
    • Argout, X.1    Salse, J.2    Aury, J.-M.3
  • 25
    • 79951828683 scopus 로고    scopus 로고
    • De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification
    • Garg R, Patel RK, Tyagi AK, et al. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 2011b;18:53-63.
    • (2011) DNA Res , vol.18 , pp. 53-63
    • Garg, R.1    Patel, R.K.2    Tyagi, A.K.3
  • 26
    • 84862956715 scopus 로고    scopus 로고
    • Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
    • Varshney RK, Chen W, Li Y, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 2012;30:83-89.
    • (2012) Nat Biotechnol , vol.30 , pp. 83-89
    • Varshney, R.K.1    Chen, W.2    Li, Y.3
  • 27
    • 79958796623 scopus 로고    scopus 로고
    • Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L)
    • Dubey A, Farmer A, Schlueter J, et al. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Res 2011;18:153-64.
    • (2011) DNA Res , vol.18 , pp. 153-164
    • Dubey, A.1    Farmer, A.2    Schlueter, J.3
  • 28
    • 84863135476 scopus 로고    scopus 로고
    • A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms
    • doi: 10.1093/mp/ssr111
    • Kudapa H, Bharti AK, Cannon SB, et al. A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms. Mol Plant 2012; doi:10.1093/mp/ssr111.
    • (2012) Mol Plant
    • Kudapa, H.1    Bharti, A.K.2    Cannon, S.B.3
  • 29
    • 79958165589 scopus 로고    scopus 로고
    • De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)
    • Al-Dous EK, George B, Al-Mahmoud ME, et al. De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 2011;29:521-7.
    • (2011) Nat Biotechnol , vol.29 , pp. 521-527
    • Al-Dous, E.K.1    George, B.2    Al-Mahmoud, M.E.3
  • 30
    • 79955769112 scopus 로고    scopus 로고
    • Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
    • Franssen SU, Shrestha RP, Bräutigam A, et al. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. BMCGenomics 2011;12:227.
    • (2011) BMC Genomics , vol.12 , pp. 227
    • Franssen, S.U.1    Shrestha, R.P.2    Bräutigam, A.3
  • 31
    • 53949113588 scopus 로고    scopus 로고
    • Single-molecule DNA sequencing technologies for future genomics research
    • Gupta PK. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 2009;26: 602-11.
    • (2009) Trends Biotechnol , vol.26 , pp. 602-611
    • Gupta, P.K.1
  • 32
    • 77950630162 scopus 로고    scopus 로고
    • Recent advances in single-molecule sequencing
    • Treffer R, Deckert V. Recent advances in single-molecule sequencing. Curr Opin Biotechnol 2010;21:1-8.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 1-8
    • Treffer, R.1    Deckert, V.2
  • 33
    • 0037474152 scopus 로고    scopus 로고
    • Zero-mode waveguides for single-molecule analysis at high concentrations
    • Levene MJ, Korlach J, Turner SW, et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003;299:682-6.
    • (2003) Science , vol.299 , pp. 682-686
    • Levene, M.J.1    Korlach, J.2    Turner, S.W.3
  • 34
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009;323:133-8.
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1    Fehr, A.2    Gray, J.3
  • 35
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: advances, challenges and opportunities
    • Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011a;12: 87-98.
    • (2011) Nat Rev Genet , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 36
    • 79960072102 scopus 로고    scopus 로고
    • Transcriptome profiling using single molecule direct RNA sequencing
    • Ozsolak F, Milos PM. Transcriptome profiling using single molecule direct RNA sequencing. Methods Mol Biol 2011b; 733:51-61.
    • (2011) Methods Mol Biol , vol.733 , pp. 51-61
    • Ozsolak, F.1    Milos, P.M.2
  • 37
    • 0037388048 scopus 로고    scopus 로고
    • Sequence information can be obtained from single DNA molecules
    • Braslavsky I, Hebert B, Kartalov E, et al. Sequence information can be obtained from single DNA molecules. Proc Natl Acad SciUSA 2003;100:3960-4.
    • (2003) Proc Natl Acad SciUSA , vol.100 , pp. 3960-3964
    • Braslavsky, I.1    Hebert, B.2    Kartalov, E.3
  • 38
    • 70249089090 scopus 로고    scopus 로고
    • Single-molecule sequencing of an individual human genome
    • Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nat Biotechnol 2009;27:847-50.
    • (2009) Nat Biotechnol , vol.27 , pp. 847-850
    • Pushkarev, D.1    Neff, N.F.2    Quake, S.R.3
  • 39
    • 41749104588 scopus 로고    scopus 로고
    • Single molecule DNA sequencing of a viral genome
    • Harris TD, Buzby PR, Babcock H, et al. Single molecule DNA sequencing of a viral genome. Science 2008;320: 106-9.
    • (2008) Science , vol.320 , pp. 106-109
    • Harris, T.D.1    Buzby, P.R.2    Babcock, H.3
  • 40
    • 67650500019 scopus 로고    scopus 로고
    • Quantification of the yeast transcriptome by single-molecule sequencing
    • Lipson D, Raz T, Kieu A, et al. Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 2009;27:652-8.
    • (2009) Nat Biotechnol , vol.27 , pp. 652-658
    • Lipson, D.1    Raz, T.2    Kieu, A.3
  • 41
    • 79960597679 scopus 로고    scopus 로고
    • An integrated semiconductor device enabling non-optical genome sequencing
    • Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475:348-52.
    • (2011) Nature , vol.475 , pp. 348-352
    • Rothberg, J.M.1    Hinz, W.2    Rearick, T.M.3
  • 42
    • 79751533742 scopus 로고    scopus 로고
    • Crop genome sequencing: lessons and rationales
    • Feuillet C, Leach JE, Rogers J, et al. Crop genome sequencing: lessons and rationales. Trends Plant Sci 2011;16:77-88.
    • (2011) Trends Plant Sci , vol.16 , pp. 77-88
    • Feuillet, C.1    Leach, J.E.2    Rogers, J.3
  • 43
    • 0037267048 scopus 로고    scopus 로고
    • Whole-genome sequence assembly for mammalian genomes: Arachne 2
    • Jaffe DB, Butler J, Gnerre S, et al. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003;13:91-96.
    • (2003) Genome Res , vol.13 , pp. 91-96
    • Jaffe, D.B.1    Butler, J.2    Gnerre, S.3
  • 44
    • 77954526823 scopus 로고    scopus 로고
    • The case for cloud computing in genome informatics
    • Stein LD. The case for cloud computing in genome informatics. Genome Biol 2010;11:207.
    • (2010) Genome Biol , vol.11 , pp. 207
    • Stein, L.D.1
  • 45
    • 79955565301 scopus 로고    scopus 로고
    • Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize
    • Poland JA, Bradbury PJ, Buckler ES, et al. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci USA 2011; 108:6893-8.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 6893-6898
    • Poland, J.A.1    Bradbury, P.J.2    Buckler, E.S.3
  • 46
    • 77951987956 scopus 로고    scopus 로고
    • Genomic selection in plant breeding: from theory to practice
    • Jannink J-L, Lorenz AJ, Iwata H. Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 2010;9:166-77.
    • (2010) Brief Funct Genomics , vol.9 , pp. 166-177
    • Jannink, J.-L.1    Lorenz, A.J.2    Iwata, H.3


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