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Volumn 30, Issue 2, 2012, Pages 1143-1153

Comparative transcriptome analysis of Pima and Acala cotton during boll development using 454 pyrosequencing technology

Author keywords

Boll development; Cotton; Pyrosequencing; Transcriptome

Indexed keywords

COTTON FIBERS; GENE EXPRESSION;

EID: 84865434476     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-012-9702-2     Document Type: Article
Times cited : (9)

References (57)
  • 1
    • 0345071423 scopus 로고    scopus 로고
    • Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing
    • Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100: 4649-4654.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4649-4654
    • Adams, K.L.1    Cronn, R.2    Percifield, R.3    Wendel, J.F.4
  • 2
    • 46149102513 scopus 로고    scopus 로고
    • Double feature selection and cluster analyses in mining of microarray data from cotton
    • Alabady MS, Youn E, Wilkins TA (2008) Double feature selection and cluster analyses in mining of microarray data from cotton. BMC Genomics 9: 295.
    • (2008) BMC Genomics , vol.9 , pp. 295
    • Alabady, M.S.1    Youn, E.2    Wilkins, T.A.3
  • 4
    • 35248812911 scopus 로고    scopus 로고
    • Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton
    • An C, Saha S, Jenkins J, Scheffler B, Wilkins T, Stelly D (2007) Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278: 539-553.
    • (2007) Mol Genet Genomics , vol.278 , pp. 539-553
    • An, C.1    Saha, S.2    Jenkins, J.3    Scheffler, B.4    Wilkins, T.5    Stelly, D.6
  • 6
    • 67649085779 scopus 로고    scopus 로고
    • Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection
    • Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE (2009) Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 9: 51.
    • (2009) BMC Plant Biol , vol.9 , pp. 51
    • Barakat, A.1    Diloreto, D.S.2    Zhang, Y.3    Smith, C.4    Baier, K.5    Powell, W.A.6    Wheeler, N.7    Sederoff, R.8    Carlson, J.E.9
  • 8
    • 80052649001 scopus 로고    scopus 로고
    • Aberrant expression of critical genes during secondary cell wall biogenesis in a cotton mutant, Ligon Lintless-1 (Li-1)
    • Bolton JJ, Soliman KM, Wilkins TA, Jenkins JN (2009) Aberrant expression of critical genes during secondary cell wall biogenesis in a cotton mutant, Ligon Lintless-1 (Li-1). Comp Funct Genomics 2009: 659301.
    • (2009) Comp Funct Genomics , vol.2009 , pp. 659301
    • Bolton, J.J.1    Soliman, K.M.2    Wilkins, T.A.3    Jenkins, J.N.4
  • 9
    • 70349439080 scopus 로고    scopus 로고
    • Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources
    • Campbell BT, Williams VE, Park W (2009) Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resources. Euphytica 169: 285-301.
    • (2009) Euphytica , vol.169 , pp. 285-301
    • Campbell, B.T.1    Williams, V.E.2    Park, W.3
  • 10
    • 51249089213 scopus 로고    scopus 로고
    • Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense
    • Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF (2008) Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evol Dev 10: 567-582.
    • (2008) Evol Dev , vol.10 , pp. 567-582
    • Chaudhary, B.1    Hovav, R.2    Rapp, R.3    Verma, N.4    Udall, J.A.5    Wendel, J.F.6
  • 11
    • 69549112933 scopus 로고    scopus 로고
    • Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)
    • Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF (2009) Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 10: 378.
    • (2009) BMC Genomics , vol.10 , pp. 378
    • Chaudhary, B.1    Hovav, R.2    Flagel, L.3    Mittler, R.4    Wendel, J.F.5
  • 12
    • 33751017957 scopus 로고    scopus 로고
    • Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
    • Cheung F, Haas B, Goldberg S, May G, Xiao Y, Town C (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7: 272.
    • (2006) BMC Genomics , vol.7 , pp. 272
    • Cheung, F.1    Haas, B.2    Goldberg, S.3    May, G.4    Xiao, Y.5    Town, C.6
  • 13
    • 79952702581 scopus 로고    scopus 로고
    • Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L.) through comparative microarray analysis
    • Curtiss J, Rudriguez-Urbe L, Stewart JM, Zhang JF (2011) Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L.) through comparative microarray analysis. BMC Plant Biol 11: 49.
    • (2011) BMC Plant Biol , vol.11 , pp. 49
    • Curtiss, J.1    Rudriguez-Urbe, L.2    Stewart, J.M.3    Zhang, J.F.4
  • 14
    • 2442609706 scopus 로고    scopus 로고
    • Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum
    • Dowd C, Wilson IW, McFadden H (2004) Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum. Mol Plant Microbe Interact 17: 654-667.
    • (2004) Mol Plant Microbe Interact , vol.17 , pp. 654-667
    • Dowd, C.1    Wilson, I.W.2    McFadden, H.3
  • 16
    • 33845984917 scopus 로고    scopus 로고
    • Gene discovery and annotation using LCM-454 transcriptome sequencing
    • Emrich SJ, Barbazuk WB, Li L, Schnable PS (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
  • 17
    • 77950931393 scopus 로고    scopus 로고
    • Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
    • Flagel LE, Wendel JF (2010) Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol 186: 184-193.
    • (2010) New Phytol , vol.186 , pp. 184-193
    • Flagel, L.E.1    Wendel, J.F.2
  • 18
    • 30544440501 scopus 로고    scopus 로고
    • Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton
    • Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112: 430-439.
    • (2006) Theor Appl Genet , vol.112 , pp. 430-439
    • Han, Z.1    Wang, C.2    Song, X.3    Guo, W.4    Gou, J.5    Li, C.6    Chen, X.7    Zhang, T.8
  • 21
    • 77953134186 scopus 로고    scopus 로고
    • Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling
    • Hinchliffe DJ, Meredith WR, Yeater KM, Kim HJ, Woodward AW, Chen ZJ, Triplett BA (2010) Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling. Theor Appl Genet 120: 1347-1366.
    • (2010) Theor Appl Genet , vol.120 , pp. 1347-1366
    • Hinchliffe, D.J.1    Meredith, W.R.2    Yeater, K.M.3    Kim, H.J.4    Woodward, A.W.5    Chen, Z.J.6    Triplett, B.A.7
  • 22
    • 52049088237 scopus 로고    scopus 로고
    • Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton
    • Hovav R, Chaudhary B, Udall JA, Flagel L, Wendel JF (2008a) Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genet 179: 1725-1733.
    • (2008) Genet , vol.179 , pp. 1725-1733
    • Hovav, R.1    Chaudhary, B.2    Udall, J.A.3    Flagel, L.4    Wendel, J.F.5
  • 23
    • 40149107790 scopus 로고    scopus 로고
    • A majority of cotton genes are expressed in single-celled fiber
    • Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF (2008b) A majority of cotton genes are expressed in single-celled fiber. Planta 227: 319-329.
    • (2008) Planta , vol.227 , pp. 319-329
    • Hovav, R.1    Udall, J.A.2    Hovav, E.3    Rapp, R.4    Flagel, L.5    Wendel, J.F.6
  • 24
    • 85047683189 scopus 로고    scopus 로고
    • Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis
    • Kim HJ, Triplett BA (2001) Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol 127: 1361-1366.
    • (2001) Plant Physiol , vol.127 , pp. 1361-1366
    • Kim, H.J.1    Triplett, B.A.2
  • 26
    • 36448974919 scopus 로고    scopus 로고
    • Gene expression changes and early events in cotton fibre development
    • Lee JJ, Woodward AW, Chen ZJ (2007) Gene expression changes and early events in cotton fibre development. Ann Bot 100: 1391-1401.
    • (2007) Ann Bot , vol.100 , pp. 1391-1401
    • Lee, J.J.1    Woodward, A.W.2    Chen, Z.J.3
  • 28
    • 70349195875 scopus 로고    scopus 로고
    • DNA polymorphisms of genes involved in fiber development in a selected set of cultivated tetraploid cotton
    • Lu Y, Curtiss J, Percy PG, Hughs SE, Yu S, Zhang JF (2009) DNA polymorphisms of genes involved in fiber development in a selected set of cultivated tetraploid cotton. Crop Sci 49: 1695-1704.
    • (2009) Crop Sci , vol.49 , pp. 1695-1704
    • Lu, Y.1    Curtiss, J.2    Percy, P.G.3    Hughs, S.E.4    Yu, S.5    Zhang, J.F.6
  • 30
    • 85167510667 scopus 로고    scopus 로고
    • SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in Amaranth
    • Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in Amaranth. Plant Genome 2: 260-270.
    • (2009) Plant Genome , vol.2 , pp. 260-270
    • Maughan, P.J.1    Yourstone, S.M.2    Jellen, E.N.3    Udall, J.A.4
  • 31
    • 33645109434 scopus 로고    scopus 로고
    • Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) genes expressed during infection of cotton (Gossypium hirsutum)
    • McFadden HG, Wilson IW, Chapple RM, Dowd C (2006) Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) genes expressed during infection of cotton (Gossypium hirsutum). Mol Plant Pathol 7: 87-101.
    • (2006) Mol Plant Pathol , vol.7 , pp. 87-101
    • McFadden, H.G.1    Wilson, I.W.2    Chapple, R.M.3    Dowd, C.4
  • 32
    • 67649867440 scopus 로고    scopus 로고
    • Detection and interpretation of expression quantitative trait loci (eQTL)
    • Michaelson JJ, Loguercio S, Beyer A (2009) Detection and interpretation of expression quantitative trait loci (eQTL). Methods 48: 265-276.
    • (2009) Methods , vol.48 , pp. 265-276
    • Michaelson, J.J.1    Loguercio, S.2    Beyer, A.3
  • 33
    • 53649088131 scopus 로고    scopus 로고
    • Application of next-generation sequencing technologies in functional genomics
    • Morozova O, Marra MA (2008) Application of next-generation sequencing technologies in functional genomics. Genomics 92: 225-264.
    • (2008) Genomics , vol.92 , pp. 225-264
    • Morozova, O.1    Marra, M.A.2
  • 35
    • 80755176300 scopus 로고    scopus 로고
    • A mini-scale hot borate method for the isolation of total RNA from a large number of cotton tissue samples
    • Pang MX, Stewart JMcD, Zhang JF (2011) A mini-scale hot borate method for the isolation of total RNA from a large number of cotton tissue samples. Afr J Biotech 10: 15430-15437.
    • (2011) Afr J Biotech , vol.10 , pp. 15430-15437
    • Pang, M.X.1    Stewart, J.2    Zhang, J.F.3
  • 36
    • 33646443638 scopus 로고    scopus 로고
    • Genetic variation for agronomic and fiber properties in an introgressed recombinant inbred population of cotton
    • Percy RG, Cantrell RG, Zhang JF (2006) Genetic variation for agronomic and fiber properties in an introgressed recombinant inbred population of cotton. Crop Sci 46: 1311-1317.
    • (2006) Crop Sci , vol.46 , pp. 1311-1317
    • Percy, R.G.1    Cantrell, R.G.2    Zhang, J.F.3
  • 37
    • 0020560945 scopus 로고
    • A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing
    • Putney SD, Herlihy WC, Schimmel P (1983) A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302: 718-721.
    • (1983) Nature , vol.302 , pp. 718-721
    • Putney, S.D.1    Herlihy, W.C.2    Schimmel, P.3
  • 39
    • 33745462176 scopus 로고    scopus 로고
    • Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation
    • Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18: 651-664.
    • (2006) Plant Cell , vol.18 , pp. 651-664
    • Shi, Y.H.1    Zhu, S.W.2    Mao, X.Z.3    Feng, J.X.4    Qin, Y.M.5    Zhang, L.6    Cheng, J.7    Wei, L.P.8    Wang, Z.Y.9    Zhu, Y.X.10
  • 41
    • 0042201892 scopus 로고    scopus 로고
    • Mining single-nucleotide polymorphisms from hexaploid wheat ESTs
    • Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49: 431-437.
    • (2003) Genome , vol.49 , pp. 431-437
    • Somers, D.J.1    Kirkpatrick, R.2    Moniwa, M.3    Walsh, A.4
  • 43
    • 60349107679 scopus 로고    scopus 로고
    • Expression of genes associated with carbohydrate metabolism in cotton stems and roots
    • Taliercio EW, Romano G, Scheffler J, Ayre BG (2009) Expression of genes associated with carbohydrate metabolism in cotton stems and roots. BMC Plant Biol 9: 11.
    • (2009) BMC Plant Biol , vol.9 , pp. 11
    • Taliercio, E.W.1    Romano, G.2    Scheffler, J.3    Ayre, B.G.4
  • 44
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 47
    • 0028072757 scopus 로고
    • A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.)
    • Wan CY, Wilkins TA (1994) A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypium hirsutum L.). Anal Biochem 223: 7-12.
    • (1994) Anal Biochem , vol.223 , pp. 7-12
    • Wan, C.Y.1    Wilkins, T.A.2
  • 48
    • 34250666153 scopus 로고    scopus 로고
    • Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing
    • Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32-42.
    • (2007) Plant Physiol , vol.144 , pp. 32-42
    • Weber, A.P.M.1    Weber, K.L.2    Carr, K.3    Wilkerson, C.4    Ohlrogge, J.B.5
  • 49
    • 0001632947 scopus 로고
    • New world tetraploid cottons contain Old World cytoplasm
    • Wendel JF (1989) New world tetraploid cottons contain Old World cytoplasm. Proc Natl Acad Sci USA 86: 4132-4136.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 4132-4136
    • Wendel, J.F.1
  • 50
    • 28344453079 scopus 로고    scopus 로고
    • Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling
    • Wu Y, Rozenfeld S, Defferrard A, Ruggiero K, Udall JA, Kim H, Llewellyn DJ, Dennis ES (2005) Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling. Mol Genet Genomics 274: 477-493.
    • (2005) Mol Genet Genomics , vol.274 , pp. 477-493
    • Wu, Y.1    Rozenfeld, S.2    Defferrard, A.3    Ruggiero, K.4    Udall, J.A.5    Kim, H.6    Llewellyn, D.J.7    Dennis, E.S.8
  • 51
    • 35348862983 scopus 로고    scopus 로고
    • Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules
    • Wu Y, Llewellyn DJ, White R, Ruggiero K, Al-Ghazi Y, Dennis ES (2007) Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules. Planta 226: 1475-1490.
    • (2007) Planta , vol.226 , pp. 1475-1490
    • Wu, Y.1    Llewellyn, D.J.2    White, R.3    Ruggiero, K.4    Al-Ghazi, Y.5    Dennis, E.S.6
  • 52
    • 41149093526 scopus 로고    scopus 로고
    • Identification of differentially expressed genes associated with cotton fiber development in a chromosomal substitution line (CS-B22sh)
    • Wu Z, Soliman KM, Bolton JJ, Saha S, Jenkins JN (2008) Identification of differentially expressed genes associated with cotton fiber development in a chromosomal substitution line (CS-B22sh). Funct Integr Genomics 8: 165-174.
    • (2008) Funct Integr Genomics , vol.8 , pp. 165-174
    • Wu, Z.1    Soliman, K.M.2    Bolton, J.J.3    Saha, S.4    Jenkins, J.N.5
  • 53
    • 33747037492 scopus 로고    scopus 로고
    • Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton
    • Yang SS, Cheung F, Lee JJ, Ha M, Wei EN, Sze S-H, Stelly DM, Thaxton PM, Triplett BA, Town CD, Chen ZJ (2006) Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J 47: 761-775.
    • (2006) Plant J , vol.47 , pp. 761-775
    • Yang, S.S.1    Cheung, F.2    Lee, J.J.3    Ha, M.4    Wei, E.N.5    Sze, S.-H.6    Stelly, D.M.7    Thaxton, P.M.8    Triplett, B.A.9    Town, C.D.10    Chen, Z.J.11
  • 54
    • 84871901610 scopus 로고    scopus 로고
    • Improving upland cotton, Gossypium hirsutum by introducing desirable genes from G. barbadense
    • 10-14 Sept. 2007, Lubbock, TX, USA, DVD, Omin Press
    • Zhang JF, Percy RG (2007) Improving upland cotton, Gossypium hirsutum by introducing desirable genes from G. barbadense. In: Proceedings of world cotton research conference-4, 10-14 Sept. 2007, Lubbock, TX, USA, DVD, Omin Press.
    • (2007) Proceedings of World Cotton Research Conference-4
    • Zhang, J.F.1    Percy, R.G.2
  • 55
    • 0000129740 scopus 로고    scopus 로고
    • Economic and rapid method for extracting cotton genomic DNA
    • Zhang JF, Stewart JM (2000) Economic and rapid method for extracting cotton genomic DNA. J Cotton Sci 4: 193-201.
    • (2000) J Cotton Sci , vol.4 , pp. 193-201
    • Zhang, J.F.1    Stewart, J.M.2
  • 56
    • 22844447428 scopus 로고    scopus 로고
    • Molecular marker diversity and field performance in commercial cotton in the Southwest US
    • Zhang JF, Lu Y, Hughs E, Cantrell RG (2005a) Molecular marker diversity and field performance in commercial cotton in the Southwest US. Crop Sci 45: 1483-1490.
    • (2005) Crop Sci , vol.45 , pp. 1483-1490
    • Zhang, J.F.1    Lu, Y.2    Hughs, E.3    Cantrell, R.G.4
  • 57
    • 27644543105 scopus 로고    scopus 로고
    • Genetic improvement of New Mexico Acala cotton germplasm and their genetic diversity
    • Zhang JF, Lu Y, Adragna H, Hughs E (2005b) Genetic improvement of New Mexico Acala cotton germplasm and their genetic diversity. Crop Sci 45: 2363-2373.
    • (2005) Crop Sci , vol.45 , pp. 2363-2373
    • Zhang, J.F.1    Lu, Y.2    Adragna, H.3    Hughs, E.4


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