-
1
-
-
84880441728
-
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
-
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
-
3
-
-
77749243220
-
-
(ed. Paterson, A.H.) Springer, New York
-
Wendel, J., Brubaker, C., Alvarez, I., Cronn, R. & Stewart, J.M. in Genetics and Genomics of Cotton, vol. 3 (ed. Paterson, A.H.) 3-22 (Springer, New York, 2009).
-
(2009)
Genetics and Genomics of Cotton
, vol.3
, pp. 3-22
-
-
Wendel, J.1
Brubaker, C.2
Alvarez, I.3
Cronn, R.4
Stewart, J.M.5
-
4
-
-
84871428041
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
18
-
-
38849147068
-
Recent advances in cotton genomics
-
Zhang, H.B., Li, Y., Wang, B. & Chee, P.W. Recent advances in cotton genomics. Int. J. Plant Genomics 2008, 742304 (2008).
-
(2008)
Int. J. Plant Genomics
, vol.2008
, pp. 742304
-
-
Zhang, H.B.1
Li, Y.2
Wang, B.3
Chee, P.W.4
-
19
-
-
34848886909
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
39
-
-
84899707486
-
The cell biology of cellulose synthesis
-
McFarlane, H.E., Doring, A. & Persson, S. The cell biology of cellulose synthesis. Annu. Rev. Plant Biol. 65, 69-94 (2014).
-
(2014)
Annu. Rev. Plant Biol
, vol.65
, pp. 69-94
-
-
McFarlane, H.E.1
Doring, A.2
Persson, S.3
-
40
-
-
0037967231
-
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
-
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
-
42
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578-579 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
43
-
-
7344254829
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|