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Volumn 33, Issue 5, 2015, Pages 524-530

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(43)  Li, Fuguang a   Fan, Guangyi b   Lu, Cairui a   Xiao, Guanghui c,d   Zou, Changsong a   Kohel, Russell J e   Ma, Zhiying f   Shang, Haihong a   Ma, Xiongfeng a   Wu, Jianyong a   Liang, Xinming b   Huang, Gai c,d   Percy, Richard G e   Liu, Kun a   Yang, Weihua a   Chen, Wenbin b   Du, Xiongming a   Shi, Chengcheng b   Yuan, Youlu a   Ye, Wuwei a   more..


Author keywords

[No Author keywords available]

Indexed keywords

GENES; PLANTS (BOTANY);

EID: 84929152065     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3208     Document Type: Article
Times cited : (896)

References (59)
  • 1
    • 84880441728 scopus 로고    scopus 로고
    • Gossypium raimondii genome, a huge leap forward in cotton genomics
    • Zhu, Y.-X. & Li, F.G. The Gossypium raimondii genome, a huge leap forward in cotton genomics. J. Integr. Plant Biol. 55, 570-571 (2013).
    • (2013) J. Integr. Plant Biol , vol.55 , pp. 570-571
    • Zhu, Y.-X.1    The, G. L.F.2
  • 2
    • 37249036997 scopus 로고    scopus 로고
    • Toward sequencing cotton (Gossypium) genomes
    • Chen, Z.J. et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1303-1310 (2007).
    • (2007) Plant Physiol , vol.145 , pp. 1303-1310
    • Chen, Z.J.1
  • 4
    • 84871428041 scopus 로고    scopus 로고
    • Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
    • Paterson, A.H. et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492, 423-427 (2012).
    • (2012) Nature , vol.492 , pp. 423-427
    • Paterson, A.H.1
  • 5
    • 84901653166 scopus 로고    scopus 로고
    • Genome sequence of the cultivated cotton Gossypium arboreum
    • Li, F.G. et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46, 567-572 (2014).
    • (2014) Nat. Genet , vol.46 , pp. 567-572
    • Li, F.G.1
  • 6
    • 84866941666 scopus 로고    scopus 로고
    • The draft genome of a diploid cotton Gossypium raimondii
    • Wang, K. et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44, 1098-1103 (2012).
    • (2012) Nat. Genet , vol.44 , pp. 1098-1103
    • Wang, K.1
  • 7
    • 0000224426 scopus 로고
    • Phylogenetics of the cotton genus (Gossypium): Character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications
    • Wendel, J.F. & Albert, V.A. Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst. Bot. 17, 115-143 (1992).
    • (1992) Syst. Bot , vol.17 , pp. 115-143
    • Wendel, J.F.1    Albert, V.A.2
  • 8
    • 0001632947 scopus 로고
    • New world tetraploid cottons contain old-world cytoplasm
    • Wendel, J.F. New world tetraploid cottons contain old-world cytoplasm. Proc. Natl. Acad. Sci. USA 86, 4132-4136 (1989).
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 4132-4136
    • Wendel, J.F.1
  • 9
    • 84904382612 scopus 로고    scopus 로고
    • A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
    • The International Wheat Genome Sequencing Consortium
    • The International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).
    • (2014) Science , vol.345 , pp. 1251788
  • 10
    • 84906689347 scopus 로고    scopus 로고
    • Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
    • Chalhoub, B. et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345, 950-953 (2014).
    • (2014) Science , vol.345 , pp. 950-953
    • Chalhoub, B.1
  • 11
    • 0000826365 scopus 로고
    • Texas Marker-1. Description of a genetic standard for Gossypium hirsutum
    • Kohel, R.J., Richmond, T.R. & Lewis, C.F. Texas Marker-1. Description of a genetic standard for Gossypium hirsutum. Crop Sci. 10, 670-671 (1970).
    • (1970) Crop Sci , vol.10 , pp. 670-671
    • Kohel, R.J.1    Richmond, T.R.2    Lewis, C.F.3
  • 12
    • 84865747346 scopus 로고    scopus 로고
    • A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome
    • Yu, J.Z. et al. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3 (Bethesda) 2, 43-58 (2012).
    • (2012) G3 (Bethesda) , vol.2 , pp. 43-58
    • Yu, J.Z.1
  • 13
    • 51249171246 scopus 로고
    • Nuclear DNA content of some important plant species
    • Arumuganathan, K. & Earle, E.D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218 (1991).
    • (1991) Plant Mol. Biol. Rep , vol.9 , pp. 208-218
    • Arumuganathan, K.1    Earle, E.D.2
  • 14
    • 23244455953 scopus 로고    scopus 로고
    • Estimation of the nuclear DNA content of Gossypium species
    • Hendrix, B. & Stewart, J.M. Estimation of the nuclear DNA content of Gossypium species. Ann. Bot. 95, 789-797 (2005).
    • (2005) Ann. Bot , vol.95 , pp. 789-797
    • Hendrix, B.1    Stewart, J.M.2
  • 15
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and de novo assembly of the giant panda genome
    • Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
    • (2010) Nature , vol.463 , pp. 311-317
    • Li, R.1
  • 16
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
    • (2010) Genome Res , vol.20 , pp. 265-272
    • Li, R.1
  • 19
    • 34848886909 scopus 로고    scopus 로고
    • The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    • Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467 (2007).
    • (2007) Nature , vol.449 , pp. 463-467
    • Jaillon, O.1
  • 20
    • 79251632958 scopus 로고    scopus 로고
    • The genome of Theobroma cacao
    • Argout, X. et al. The genome of Theobroma cacao. Nat. Genet. 43, 101-108 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 101-108
    • Argout, X.1
  • 21
    • 84903203459 scopus 로고    scopus 로고
    • The genome of Eucalyptus grandis
    • Myburg, A.A. et al. The genome of Eucalyptus grandis. Nature 510, 356-362 (2014).
    • (2014) Nature , vol.510 , pp. 356-362
    • Myburg, A.A.1
  • 22
    • 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 408, 796-815 (2000).
    • (2000) Nature , vol.408 , pp. 796-815
  • 23
    • 74549221016 scopus 로고    scopus 로고
    • Genome sequence of the palaeopolyploid soybean
    • Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183 (2010).
    • (2010) Nature , vol.463 , pp. 178-183
    • Schmutz, J.1
  • 24
    • 57149102681 scopus 로고    scopus 로고
    • Unravelling ancient hexaploidy through multiply-aligned angiosperm gene maps
    • Tang, H. et al. Unravelling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944-1954 (2008).
    • (2008) Genome Res , vol.18 , pp. 1944-1954
    • Tang, H.1
  • 25
    • 84892538565 scopus 로고    scopus 로고
    • Transposable elements: Powerful contributors to angiosperm evolution and diversity genome
    • Oliver, K.R., McComb, J.A. & Greene, W.K. Transposable elements: powerful contributors to angiosperm evolution and diversity genome. Genome Biol. Evol. 5, 1886-1901 (2013).
    • (2013) Genome Biol. Evol , vol.5 , pp. 1886-1901
    • Oliver, K.R.1    McComb, J.A.2    Greene, W.K.3
  • 26
    • 84899743736 scopus 로고    scopus 로고
    • The contributions of transposable elements to the structure, function, and evolution of plant genomes
    • Bennetzen, J.L. & Wang, H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 65, 505-530 (2014).
    • (2014) Annu. Rev. Plant Biol , vol.65 , pp. 505-530
    • Bennetzen, J.L.1    Wang, H.2
  • 27
    • 74849090833 scopus 로고    scopus 로고
    • The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
    • Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92-94 (2010).
    • (2010) Science , vol.327 , pp. 92-94
    • Ossowski, S.1
  • 28
    • 84929171720 scopus 로고    scopus 로고
    • Sequencing of allotetraploid cotton (Gossypium hirsutum L. Acc. TM-1) provides a resource for fiber improvement
    • 20 April
    • Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol. doi:10.1038/nbt.3207 (20 April 2015).
    • (2015) Nat Biotechnol
    • Zhang, T.1
  • 29
    • 42549120705 scopus 로고    scopus 로고
    • Synteny and collinearity in plant genomes
    • Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486-488 (2008).
    • (2008) Science , vol.320 , pp. 486-488
    • Tang, H.1
  • 30
    • 15544383703 scopus 로고    scopus 로고
    • Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L
    • Udall, J.A., Quijada, P.A. & Osborn, T.C. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 169, 967-979 (2005).
    • (2005) Genetics , vol.169 , pp. 967-979
    • Udall, J.A.1    Quijada, P.A.2    Osborn, T.C.3
  • 31
    • 0031904591 scopus 로고    scopus 로고
    • D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel venues for evolution
    • Wright, R.J., Thaxton, P.M., El-Zik, K.M. & Paterson, A.H. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel venues for evolution. Genetics 149, 1987-1996 (1998).
    • (1998) Genetics , vol.149 , pp. 1987-1996
    • Wright, R.J.1    Thaxton, P.M.2    El-Zik, K.M.3    Paterson, A.H.4
  • 32
    • 20144366003 scopus 로고    scopus 로고
    • The genomes of Oryza sativa: A history of duplications
    • Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).
    • (2005) PLoS Biol , vol.3 , pp. e38
    • Yu, J.1
  • 33
    • 0036097982 scopus 로고    scopus 로고
    • Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium)
    • Small, R.L. & Wendel, J.F. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol. Biol. Evol. 19, 597-607 (2002).
    • (2002) Mol. Biol. Evol , vol.19 , pp. 597-607
    • Small, R.L.1    Wendel, J.F.2
  • 34
    • 33745462176 scopus 로고    scopus 로고
    • Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fibre cell elongation
    • Shi, Y.H. et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fibre cell elongation. Plant Cell 18, 651-664 (2006).
    • (2006) Plant Cell , vol.18 , pp. 651-664
    • Shi, Y.H.1
  • 35
    • 37849028984 scopus 로고    scopus 로고
    • Saturated very-long-chain fatty acids promote cotton fibre and Arabidopsis cell elongation by activating ethylene biosynthesis
    • Qin, Y.M. et al. Saturated very-long-chain fatty acids promote cotton fibre and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell 19, 3692-3704 (2007).
    • (2007) Plant Cell , vol.19 , pp. 3692-3704
    • Qin, Y.M.1
  • 36
    • 78751591032 scopus 로고    scopus 로고
    • How cotton fibres elongate: A tale of linear cell-growth mode
    • Qin, Y.M. & Zhu, Y.-X. How cotton fibres elongate: a tale of linear cell-growth mode. Curr. Opin. Plant Biol. 14, 106-111 (2011).
    • (2011) Curr. Opin. Plant Biol , vol.14 , pp. 106-111
    • Qin, Y.M.1    Zhu, Y.-X.2
  • 37
    • 77956554550 scopus 로고    scopus 로고
    • Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fibre and Arabidopsis root hair elongation
    • Pang, C.Y. et al. Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fibre and Arabidopsis root hair elongation. Mol. Cell. Proteomics 9, 2019-2033 (2010).
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 2019-2033
    • Pang, C.Y.1
  • 38
    • 0037016399 scopus 로고    scopus 로고
    • Sitosterol-ß-glucoside as primer for cellulose synthesis in plants
    • Peng, L.C., Kawagoe, Y., Hogan, P. & Delmer, D. Sitosterol-ß-glucoside as primer for cellulose synthesis in plants. Science 295, 147-150 (2002).
    • (2002) Science , vol.295 , pp. 147-150
    • Peng, L.C.1    Kawagoe, Y.2    Hogan, P.3    Delmer, D.4
  • 40
    • 0037967231 scopus 로고    scopus 로고
    • Abundant gene conversion between arms of palindromes in human and ape y chromosomes
    • Rozen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873-876 (2003).
    • (2003) Nature , vol.423 , pp. 873-876
    • Rozen, S.1
  • 41
    • 84873087245 scopus 로고    scopus 로고
    • A heterozygous moth genome provides insights into herbivory and detoxification
    • You, M. et al. A heterozygous moth genome provides insights into herbivory and detoxification. Nat. Genet. 45, 220-225 (2013).
    • (2013) Nat. Genet , vol.45 , pp. 220-225
    • You, M.1
  • 43
    • 7344254829 scopus 로고
    • Construction of integrated genetic linkage maps by means of a new computer package: JoinMap
    • Stam, P. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3, 739-744 (1993).
    • (1993) Plant J. , vol.3 , pp. 739-744
    • Stam, P.1
  • 44
    • 77953796079 scopus 로고    scopus 로고
    • Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing
    • Xie, W. et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA 107, 10578-10583 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 10578-10583
    • Xie, W.1
  • 45
    • 0034284437 scopus 로고    scopus 로고
    • Repbase Update: A database and an electronic journal of repetitive elements
    • Jurka, J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418-420 (2000).
    • (2000) Trends Genet , vol.16 , pp. 418-420
    • Jurka, J.1
  • 46
    • 84860513986 scopus 로고    scopus 로고
    • PILER: Identification and classification of genomic repeats
    • Edgar, R.C. & Myers, E.W. PILER: identification and classification of genomic repeats. Bioinformatics 21 (suppl. 1), i152-i158 (2005).
    • (2005) Bioinformatics , vol.21 , pp. i152-i158
    • Edgar, R.C.1    Myers, E.W.2
  • 47
    • 34547592867 scopus 로고    scopus 로고
    • LTR-FINDER: An efficient tool for the prediction of full-length LTR retrotransposons
    • Xu, Z. & Wang, H. LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265-W268 (2007).
    • (2007) Nucleic Acids Res , vol.35 , pp. W265-W268
    • Xu, Z.1    Wang, H.2
  • 48
    • 63049126614 scopus 로고    scopus 로고
    • Using RepeatMasker to identify repetitive elements in genomic sequences
    • Chapter 4, Unit 4.10
    • Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics. Chapter 4, Unit 4.10 (2009).
    • (2009) Curr. Protoc. Bioinformatics
    • Tarailo-Graovac, M.1    Chen, N.2
  • 49
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 50
    • 34147180390 scopus 로고    scopus 로고
    • Creating a honey bee consensus gene set
    • Elsik, C.G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).
    • (2007) Genome Biol , vol.8 , pp. R13
    • Elsik, C.G.1
  • 51
    • 33747830848 scopus 로고    scopus 로고
    • AUGUSTUS: Ab initio prediction of alternative transcripts
    • Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. W435-W439
    • Stanke, M.1
  • 52
    • 8844252293 scopus 로고    scopus 로고
    • TigrScan and GlimmerHMM: Twoopen source ab initio eukaryotic gene-finders
    • Majoros, W., Pertea, M. & Salzberg, S. TigrScan and GlimmerHMM: Twoopen source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878-2879 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 2878-2879
    • Majoros, W.1    Pertea, M.2    Salzberg, S.3
  • 53
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and genomewise
    • Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988-995 (2004).
    • (2004) Genome Res , vol.14 , pp. 988-995
    • Birney, E.1    Clamp, M.2    Durbin, R.3
  • 54
    • 0036226603 scopus 로고    scopus 로고
    • BLAT: The BLAST-like alignment tool
    • Kent, W.J. BLAT: The BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 55
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 56
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556 (1997).
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 57
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm, M., Storm, C.E. & Sonnhammer, E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052 (2001).
    • (2001) J. Mol. Biol , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 58
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similarity searching
    • Finn, R.D., Clements, J. & Eddy, S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29-W37 (2011).
    • (2011) Nucleic Acids Res , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 59
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
    • (2011) Mol. Biol. Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1


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