Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Liu, Xia ^a   Zhao, Bo ^b   Zheng, Hua Jun ^c   Hu, Yan ^d   Lu, Gang ^c   Yang, Chang Qing ^b   Chen, Jie Dan ^d   Chen, Jun Jian ^a   Chen, Dian Yang ^b   Zhang, Liang ^c   Zhou, Yan ^c,e   Wang, Ling Jian ^b   Guo, Wang Zhen ^d   Bai, Yu Lin ^a   Ruan, Ju Xin ^b   Shangguan, Xiao Xia ^b   Mao, Ying Bo ^b   Shan, Chun Min ^b   Jiang, Jian Ping ^c   Zhu, Yong Qiang ^c   Jin, Lei ^c   Kang, Hui ^c   Chen, Shu Ting ^c   He, Xu Lin ^c   Wang, Rui ^c   Wang, Yue Zhu ^c   Chen, Jie ^c   Wang, Li Jun ^c   Yu, Shu Ting ^c   Wang, Bi Yun ^c   Wei, Jia ^c   Song, Si Chao ^c   Lu, Xin Yan ^c   Gao, Zheng Chao ^c   Gu, Wen Yi ^c   Deng, Xiao ^f   Ma, Dan ^d   Wang, Sen ^d   Liang, Wen Hua ^d   Fang, Lei ^d   Cai, Cai Ping ^d   Zhu, Xie Fei ^d   Zhou, Bao Liang ^d   Chen, Z Jeffrey ^d,h   Xu, Shu Hua ^g   Zhang, Yu Gao ^a   Wang, Sheng Yue ^c   Zhang, Tian Zhen ^d   Zhao, Guo Ping ^b,c,e   Chen, Xiao Ya ^b   more..

^a Esquel Group   (Hong Kong)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^d NANJING AGRICULTURAL UNIVERSITY   (China)

^e FUDAN UNIVERSITY   (China)

^f SOOCHOW UNIVERSITY   (China)

^g MAX PLANCK INSTITUTE   (Germany)

^h UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHYTOALEXINS; SESQUITERPENE; TERPENE SYNTHASE; TRANSFERASE;

BIOLOGY; CLUSTER ANALYSIS; COTTON; EVOLUTION; GENE EXPRESSION PROFILING; GENE TRANSLOCATION; GENETIC ASSOCIATION STUDY; GENETICS; GENOMICS; GOSSYPIUM; METABOLISM; METABOLOMICS; MOLECULAR GENETICS; PHENOTYPE; PHYLOGENY; PLANT CHROMOSOME; PLANT GENOME; POLYPLOIDY; PROCEDURES; QUANTITATIVE TRAIT;

ALKYL AND ARYL TRANSFERASES; BIOLOGICAL EVOLUTION; CHROMOSOMES, PLANT; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COTTON FIBER; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION STUDIES; GENOME, PLANT; GENOMICS; GOSSYPIUM; METABOLOMICS; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; PHYLOGENY; POLYPLOIDY; QUANTITATIVE TRAIT, HERITABLE; SESQUITERPENES; TRANSLOCATION, GENETIC;

EID: 84942937002     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep14139     Document Type: Article

References (68)

1. Soltis, D. E., Visger, C. J. & Soltis, P. S. The polyploidy revolution then and now: Stebbins revisited. Am J Bot. 101, 1057-1078 (2014).
2. Hegarty, M. J. & Hiscock, S. J. Genomic clues to the evolutionary success of polyploid plants. Curr Biol. 18, R435-444 (2008).
3. Otto, S. P. The evolutionary consequences of polyploidy. Cell. 131, 452-462 (2007).
4. Jiao, Y. et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 473, 97-100 (2011).
5. Renny-Byfield, S. & Wendel, J. F. Doubling down on genomes: polyploidy and crop plants. Am J Bot. 101, 1711-1725 (2014).
6. Gong, L., Kakrana, A., Arikit, S., Meyers, B. C. & Wendel, J. F. Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome biol Evol. 5, 2449-2459 (2013).
7. Hawkins, J. S., Kim, H., Nason, J. D., Wing, R. A. & Wendel, J. F. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16, 1252-1261 (2006).
8. Grover, C. et al. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack. Genet Resour Crop Ev. 62, 103-114 (2015).
9. Hendrix, B. & Stewart, J. M. Estimation of the nuclear DNA content of gossypium species. Ann Bot. 95, 789-797 (2005).
10. Paterson, A. H. et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492, 423-427 (2012).
11. Wang, K. et al. The draft genome of a diploid cotton Gossypium raimondii. Nat Genet. 44, 1098-1103 (2012).
12. Li, F. et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet. 46, 567-572 (2014).
13. Senchina, D. S. et al. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol. 20, 633-643 (2003).
14. Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science. 345, 1250092 (2014).
15. Chalhoub, B. et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 345, 950-953 (2014).
16. Kim, H. J. & Triplett, B. A. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol. 127, 1361-1366 (2001).
17. Smart, L. B., Vojdani, F., Maeshima, M. & Wilkins, T. A. Genes involved in osmoregulation during turgor-driven cell expansion of developing cotton fibers are differentially regulated. Plant Physiol. 116, 1539-1549 (1998).
18. Ruan, Y. L., Llewellyn, D. J. & Furbank, R. T. The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin. Plant Cell. 13, 47-60 (2001).
19. Wang, P. et al. Inheritance of long staple fiber quality traits of Gossypium barbadense in G. hirsutum background using CSILs. Theor Appl Genet. 124, 1415-1428 (2012).
20. Li, F. et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol. 33, 524-530 (2015).
21. Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol. 33, 531-537 (2015).
22. Wang, S. et al. Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes. Genome Biol. 16, 108 (2015).
23. Arabidopsis Genome I. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408, 796-815 (2000).
24. International Rice Genome Sequencing P. The map-based sequence of the rice genome. Nature. 436, 793-800 (2005).
25. Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature. 463, 178-183 (2010).
26. Brenchley, R. et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 491, 705-710 (2012).
27. Page, J. T. et al. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. G3. 3, 1809-1818 (2013).
28. Brubaker, C. L., Paterson, A. H. & Wendel, J. F. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome. 42, 184-203 (1999).
29. Yu, J. Z. et al. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3. 2, 43-58 (2012).
30. Nystedt, B. et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 497, 579-584 (2013).
31. SanMiguel, P. & Bennetzen, J. L. Evidence that a Recent Increase in Maize Genome Size was Caused by the Massive Amplification of Intergene Retrotransposons. Annals of Botany. 82 (suppl 1), 37-44 (1998).
32. Hawkins, J. S., Proulx, S. R., Rapp, R. A. & Wendel, J. F. Rapid D. N. A. loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. P Natl Acad Sci USA. 106, 17811-17816 (2009).
33. Zou, C., Lehti-Shiu, M. D., Thibaud-Nissen, F., Prakash, T., Buell, C. R. & Shiu, S. H. Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol. 151, 3-15 (2009).
34. Yoo, M. J. & Wendel, J. F. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet. 10, e1004073 (2014).
35. Walford, S. A., Wu, Y., Llewellyn, D. J. & Dennis, E. S. GhMYB25-like: a key factor in early cotton fibre development. Plant J. 65, 785-797 (2011).
36. Zhang, M. et al. Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat Biotechnol. 29, 453-458 (2011).
37. Shan, C. M. et al. Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3. Nat Commun. 5, 5519 (2014).
38. Chen, Z. J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol. 58, 377-406 (2007).
39. Bai, M. Y., Fan, M., Oh, E. & Wang, Z. Y. A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis. Plant Cell. 24, 4917-4929 (2012).
40. Zhang, L. Y. et al. Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell. 21, 3767-3780 (2009).
41. Argout, X. et al. The genome of Theobroma cacao. Nat Genet. 43, 101-108 (2011).
42. Gu, Y. et al. Identification of a cellulose synthase-associated protein required for cellulose biosynthesis. P Natl Acad Sci USA. 107, 12866-12871 (2010).
43. McFarlane, H. E., Doring, A. & Persson, S. The cell biology of cellulose synthesis. Annu Rev Plant Biol. 65, 69-94 (2014).
44. Gou, J. Y., Wang, L. J., Chen, S. P., Hu, W. L. & Chen, X. Y. Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res. 17, 422-434 (2007).
45. Pear, J. R., Kawagoe, Y., Schreckengost, W. E. & Delmer, D. P., Stalker DM. Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. P Natl Acad Sci USA. 93, 12637-12642 (1996).
46. Taylor-Teeples, M. et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 517, 571-575 (2015).
47. Mao, Y. B. et al. Silencing a cotton bollworm P450 monooxygenase gene by plant-mediated RNAi impairs larval tolerance of gossypol. Nat Biotechnol. 25, 1307-1313 (2007).
48. Tao, X. Y., Xue, X. Y., Huang, Y. P., Chen, X. Y. & Mao, Y. B. Gossypol-enhanced P450 gene pool contributes to cotton bollworm tolerance to a pyrethroid insecticide. Mol Ecol. 21, 4371-4385 (2012).
49. Bohlmann, J., Meyer-Gauen, G. & Croteau, R. Plant terpenoid synthases: molecular biology and phylogenetic analysis. P Natl Acad Sci USA. 95, 4126-4133 (1998).
50. Chen, X. Y., Chen, Y., Heinstein, P. & Davisson, V. J. Cloning, expression, and characterization of (+)-delta-cadinene synthase: a catalyst for cotton phytoalexin biosynthesis. Arch Biochem Biophys. 324, 255-266 (1995).
51. Comai, L. et al. Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell. 12, 1551-1568 (2000).
52. Liu, B. & Wendel, J. F. Non-Mendelian phenomenon in allopolyploid genome evolution. Curr Genomics. 3, 489-505 (2002).
53. Adams, K. L. & Wendel, J. F. Novel patterns of gene expression in polyploid plants. Trends Genet. 21, 539-543 (2005).
54. Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O. & Borodovsky, M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res. 33, 6494-6506 (2005).
55. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 19 Suppl 2, ii215-225 (2003).
56. Salamov, A. A. & Solovyev, V. V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000).
57. Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M. & Robles, M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 21, 3674-3676 (2005).
58. Jin, J., Zhang, H., Kong, L., Gao, G. & Luo, J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 42, D1182-1187 (2014).
59. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277-280 (2004).
60. Li, L., Stoeckert, C. J., Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
61. Zhang, Z., Li, J., Zhao, X. Q., Wang, J., Wong, G. K. & Yu, J. KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, proteomics & bioinformatics. 4, 259-263 (2006).
62. Xu, Z. & Wang, H. LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265-268 (2007).
63. Han, Y. & Wessler, S. R. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199 (2010).
64. Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8, 973-982 (2007).
65. Zhang, Z., Carriero, N., Zheng, D., Karro, J., Harrison, P. M. & Gerstein, M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 22, 1437-1439 (2006).
66. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
67. Wang, L., Feng, Z., Wang, X., Wang, X. & Zhang, X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 26, 136-138 (2010).
68. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 5, 621-628 (2008).