Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of gossypium barbadense L

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Yuan, Daojun ^a   Tu, Lili ^a   Zhang, Xianlong ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; CONTROLLED STUDY; COTTON; CYTOSKELETON; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRAIT; GENETIC VARIABILITY; GOSSYPIUM BARBADENSE; HOMEOSTASIS; MICROSATELLITE MARKER; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION POTENTIAL; PLANT GENETICS; POLYPLOIDY; PROTEIN BINDING; PROTEIN MOTIF; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE; CHROMOSOME MAP; GENE LIBRARY; GENETICS; GOSSYPIUM; GROWTH, DEVELOPMENT AND AGING; HUMAN; PHENOTYPE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

GOSSYPIUM; GOSSYPIUM BARBADENSE; GOSSYPIUM HIRSUTUM;

MESSENGER RNA;

CHROMOSOME MAPPING; COTTON FIBER; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENETIC VARIATION; GOSSYPIUM; HUMANS; PHENOTYPE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 79960851454     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022758     Document Type: Article

References (85)

1. Basra AS, Malik CP, GH Bourne JFD, Jeon KW, (1984) Development of the Cotton Fiber. Int Rev Cytol 89: 65-113.
2. 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.
3. Tiwari SC, Wilkins TA, (1995) Cotton (Gossypium hirsutum) seed trichomes expand via diffuse growing mechanism. Can J Bot 73: 746-757.
4. Smart LB, Vojdani F, Maeshima M, Wilkins TA, (1998) Genes Involved in Osmoregulation during Turgor-Driven Cell Expansion of Developing Cotton Fibers Are Differentially Regulated. Plant Physiol 116: 1539-1549.
5. John ME, Keller G, (1996) Metabolic pathway engineering in cotton Biosynthesis of polyhydroxybutyrate in fiber cells. Proc Natl Acad Sci 93: 12768-12773.
6. Arumuganathan K, Earle E, (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218.
7. Ulloa M, Stewart J, Garcia-C E, Godoy-A S, Gaytan-M A, et al. (2006) Cotton Genetic Resources in the Western States of Mexico: In situ Conservation Status and Germplasm Collection for ex situ Preservation. Genet Resour Crop Evol 53: 653-668.
8. Li XB, Cai L, Cheng NH, Liu JW, (2002) Molecular characterization of the cotton GhTUB1 gene that is preferentially expressed in fiber. Plant Physiol 130: 666-674.
9. Arpat AB, Waugh M, Sullivan JP, Gonzales M, Frisch D, et al. (2004) Functional genomics of cell elongation in developing cotton fibers. Plant Mol Biol 54: 911-929.
10. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, et al. (2006) A global assembly of cotton ESTs. Genome Res 16: 441-450.
11. Yang SS, Cheung F, Lee JJ, Ha M, Wei NE, et al. (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.
12. Tu LL, Zhang XL, Liang SG, Liu DQ, Zhu LF, et al. (2007) Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber development. Plant Cell Rep 26: 1309-1320.
13. Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, et al. (2008) Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evol Dev 10: 567-582.
14. Li XB, Fan XP, Wang XL, Cai L, Yang WC, (2005) The Cotton ACTIN1 Gene Is Functionally Expressed in Fibers and Participates in Fiber Elongation. Plant Cell 17: 859-875.
15. Li L, Wang XL, Huang GQ, Li XB, (2007) Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation. J Exp Bot 58: 3227-3238.
16. Wang HY, Yu Y, Chen ZL, Xia GX, (2005) Functional characterization of Gossypium hirsutum profilin 1 gene (GhPFN1) in tobacco suspension cells. Planta 222: 594-603.
17. He XC, Qin YM, Xu Y, Hu CY, Zhu YX, (2008) Molecular cloning, expression profiling, and yeast complementation of 19 β-tubulin cDNAs from developing cotton ovules. J Exp Bot 59: 2687-2695.
18. Wang HY, Wang J, Gao P, Jiao GL, Zhao PM, et al. (2009) Down-regulation of GhADF1 gene expression affects cotton fibre properties. Plant Biotechnol J 7: 13-23.
19. Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, et al. (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18: 651-664.
20. Li HB, Qin YM, Pang Y, Song WQ, Mei WQ, et al. (2007) A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. New Phytol 175: 462-471.
21. Qin YM, Hu CY, Pang Y, Kastaniotis AJ, Hiltunen JK, et al. (2007) Saturated Very-Long-Chain Fatty Acids Promote Cotton Fiber and Arabidopsis Cell Elongation by Activating Ethylene Biosynthesis. Plant Cell 19: 3692-3704.
22. Song WQ, Qin YM, Saito M, Shirai T, Pujol FM, et al. (2009) Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif. J Exp Bot 60: 1839-1848.
23. Clark G, Torres J, Finlayson S, Guan X, Handley C, et al. (2010) Apyrase (Nucleoside Triphosphate-Diphosphohydrolase) and Extracellular Nucleotides Regulate Cotton Fiber Elongation in Cultured Ovules. Plant Physiol 152: 1073-1083.
24. Al-Ghazi Y, Bourot S, Arioli T, Dennis ES, Llewellyn DJ, (2009) Transcript Profiling During Fiber Development Identifies Pathways in Secondary Metabolism and Cell Wall Structure That May Contribute to Cotton Fiber Quality. Plant Cell Physiol 50: 1364-1381.
25. Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, et al. (2008) The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet 4: e25.
26. Zhang D, Zhang T, Guo W, (2010) Effect of H2O2 on fiber initiation using fiber retardation initiation mutants in cotton (Gossypium hirsutum). J Plant Physiol 167: 393-399.
27. Rapp R, Haigler C, Flagel L, Hovav R, Udall J, et al. (2010) Gene expression in developing fibers of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biol 8: 139-153.
28. Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
29. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, et al. (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16: 114-125.
30. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
31. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.
32. Labarga A, Valentin F, Anderson M, Lopez R, (2007) Web services at the European Bioinformatics Institute. Nucleic Acids Res 35: W6-W11.
33. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M, (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: W182-W185.
34. Parkinson J, Blaxter M, (2003) SimiTri-visualizing similarity relationships for groups of sequences. Bioinformatics 19: 390-395.
35. Girke T, Lauricha J, Tran H, Keegstra K, Raikhel N, (2004) The Cell Wall Navigator Database. A Systems-Based Approach to Organism-Unrestricted Mining of Protein Families Involved in Cell Wall Metabolism. Plant Physiol 136: 3003-3008.
36. Zhang H, Jin J, Tang L, Zhao Y, Gu X, et al. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res 39: D1114-D1117.
37. Oliveira EJ, Pádua JG, Zucchi MI, Vencovsky R, Vieira MLC, (2006) Origin, evolution and genome distribution of microsatellites. Genet Mol Biol 29: 294-307.
38. Saha M, Mian M, Eujayl I, Zwonitzer J, Wang L, et al. (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109: 783-791.
39. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, et al. (2003) How much effort is required to isolate nuclear microsatellites from plants. Mol Ecol 12: 1339-1348.
40. Yu Y, Yuan DJ, Liang SG, Li XM, Wang XQ, et al. (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12: 15.
41. Rudd S, (2003) Expressed sequence tags: alternative or complement to whole genome sequences. Trends Plant Sci 8: 321-329.
42. Li Y, Liu D, Tu L, Zhang X, Wang L, et al. (2010) Suppression of GhAGP4 gene expression repressed the initiation and elongation of cotton fiber. Plant Cell Rep 29: 193-202.
43. Huang GQ, Xu WL, Gong SY, Li B, Wang XL, et al. (2008) Characterization of 19 novel cotton FLA genes and their expression profiling in fiber development and in response to phytohormones and salt stress. Physiol Plant 134: 348-359.
44. Liu D, Tu L, Li Y, Wang L, Zhu L, et al. (2008) Genes Encoding Fasciclin-Like Arabinogalactan Proteins are Specifically Expressed During Cotton Fiber Development. Plant Mol Biol Rep 26: 98-113.
45. Chi J, Wang X, Zhou H, Zhang G, Sun Y, et al. (2008) Molecular cloning and characterization of the actin-depolymerizing factor gene in Gossypium barbadense. Genes Genet Syst 83: 383-391.
46. Li XB, Xu D, Wang XL, Huang GQ, Luo J, et al. (2010) Three cotton genes preferentially expressed in flower tissues encode actin-depolymerizing factors which are involved in F-actin dynamics in cells. J Exp Bot 61: 41-53.
47. Wang J, Wang HY, Zhao PM, Han LB, Jiao GL, et al. (2010) Over-expression of a Profilin (GhPFN2) Promotes the Progression of Developmental Phases in Cotton Fibers. Plant Cell Physiol 51: 1276-1290.
48. Xu WL, Wang XL, Wang H, Li XB, (2007) Molecular characterization and expression analysis of nine cotton GhEF1A genes encoding translation elongation factor 1A. Gene 389: 27-35.
49. Yu S, (2010) Progress in Upland cotton sequencing. International Cotton Initiative Genome(ICGI) Research Conference. Canberra.
50. Jansson S, Douglas CJ, (2007) Populus: A Model System for Plant Biology. Annu Rev Plant Biol 58: 435-458.
51. Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43: 109-116.
52. Hovav R, Udall J, Hovav E, Rapp R, Flagel L, et al. (2008) A majority of cotton genes are expressed in single-celled fiber. Planta 227: 319-329.
53. Wilkins TA, Arpat AB, (2005) The cotton fiber transcriptome. Physiol Plant 124: 295-300.
54. Xiao YH, Li DM, Yin MH, Li XB, Zhang M, et al. (2010) Gibberellin 20-oxidase promotes initiation and elongation of cotton fibers by regulating gibberellin synthesis. J Plant Physiol 167: 829-837.
55. Jin LG, Li H, Liu JY, (2010) Molecular Characterization of Three Ethylene Responsive Element Binding Factor Genes from Cotton. J Integr Plant Biol 52: 485-495.
56. Ruan YL, Xu SM, White R, Furbank RT, (2004) Genotypic and Developmental Evidence for the Role of Plasmodesmatal Regulation in Cotton Fiber Elongation Mediated by Callose Turnover. Plant Physiol 136: 4104-4113.
57. Ruan YL, Llewellyn DJ, Furbank RT, (2001) 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.
58. An C, Saha S, Jenkins JN, Scheffler BE, Wilkins TA, et al. (2007) Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Genet Genomics 278: 539-553.
59. Feng JX, Ji SJ, Shi YH, Xu Y, Wei G, et al. (2004) Analysis of five differentially expressed gene families in fast elongating cotton fiber. Acta Biochim Biophys Sin 36: 51-56.
60. Okamoto-Nakazato A, Takahashi K, Kido N, Owaribe K, Katou K, (2000) Molecular cloning of yieldins regulating the yield threshold of cowpea cell walls: cDNA cloning and characterization of recombinant yieldin. Plant Cell Environ 23: 155-164.
61. Okamoto-Nakazato A, Takahashi K, Katoh-Semba R, Katou K, (2001) Distribution of Yieldin, a Regulatory Protein of the Cell Wall Yield Threshold, in Etiolated Cowpea Seedlings. Plant Cell Rep 42: 952-958.
62. Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel J, (2009) Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 10: 378-389.
63. Foyer CH, Noctor G, (2005) Redox Homeostasis and Antioxidant Signaling: A Metabolic Interface between Stress Perception and Physiological Responses. Plant Cell 17: 1866-1875.
64. Mei W, Qin Y, Song W, Li J, Zhu Y, (2009) Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation. J Genet Genomics 36: 141-150.
65. Finkemeier I, Goodman M, Lamkemeyer P, Kandlbinder A, Sweetlove LJ, et al. (2005) The Mitochondrial Type II Peroxiredoxin F Is Essential for Redox Homeostasis and Root Growth of Arabidopsis thaliana under Stress. J Biol Chem 280: 12168-12180.
66. Moons A, Valcke R, Van Montagu M, (1998) Low-oxygen stress and water deficit induce cytosolic pyruvate orthophosphate dikinase (PPDK) expression in roots of rice, a C3 plant. Plant J 15: 89-98.
67. Weber H, Chételat A, Reymond P, Farmer EE, (2004) Selective and powerful stress gene expression in Arabidopsis in response to malondialdehyde. Plant J 37: 877-888.
68. Titiz O, Tambasco-Studart M, Warzych E, Apel K, Amrhein N, et al. (2006) PDX1 is essential for vitamin B6 biosynthesis, development and stress tolerance in Arabidopsis. Plant J 48: 933-946.
69. Jakoby MJ, Falkenhan D, Mader MT, Brininstool G, Wischnitzki E, et al. (2008) Transcriptional Profiling of Mature Arabidopsis Trichomes Reveals That NOECK Encodes the MIXTA-Like Transcriptional Regulator MYB106. Plant Physiol 148: 1583-1602.
70. Basu D, Le J, El-Essal SE-D, Huang S, Zhang C, et al. (2005) DISTORTED3/SCAR2 Is a Putative Arabidopsis WAVE Complex Subunit That Activates the Arp2/3 Complex and Is Required for Epidermal Morphogenesis. Plant Cell 17: 502-524.
71. Zolman B, Nyberg M, Bartel B, (2007) IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response. Plant Mol Biol 64: 59-72.
72. Strader LC, Culler AH, Cohen JD, Bartel B, (2010) Conversion of Endogenous Indole-3-Butyric Acid to Indole-3-Acetic Acid Drives Cell Expansion in Arabidopsis Seedlings. Plant Physiol 153: 1577-1586.
73. Davies RT, Goetz DH, Lasswell J, Anderson MN, Bartel B, (1999) IAR3 Encodes an Auxin Conjugate Hydrolase from Arabidopsis. Plant Cell 11: 365-376.
74. Ishida K, Yamashino T, Yokoyama A, Mizuno T, (2008) Three Type-B Response Regulators, ARR1, ARR10 and ARR12, Play Essential but Redundant Roles in Cytokinin Signal Transduction Throughout the Life Cycle of Arabidopsis thaliana. Plant Cell Rep 49: 47-57.
75. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
76. Ewing B, Hillier L, Wendl MC, Green P, (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
77. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, et al. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19: 651-652.
78. Zhang LD, Yuan DJ, Zhang JW, Wang SP, Zhang QF, (2003) A new method for EST clustering. Acta genetica Sinica 30: 147-153.
79. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.
80. Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
81. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
82. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, et al. (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res 36: D966-D969.
83. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
84. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34.
85. Blüthgen N, Brand K, Čajavec B, Swat M, Herzel H, et al. (2005) Biological Profiling of Gene Groups utilizing Gene Ontology. Genome Informatic 16: 106-115.