Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant

Genomics

Volumn 96, Issue 6, 2010, Pages 369-376

  Wang, Qin Qin ^a   Liu, Fei ^a   Chen, Xu Sheng ^b   Ma, Xiao Jie ^b   Zeng, Hou Qing ^a   Yang, Zhi Min ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Deep sequencing; Fiber; Gossypium hirsutum; MicroRNA target gene; Transcriptome

Indexed keywords

CELLULOSE; MUTANT PROTEIN; TRANSCRIPTOME;

ARTICLE; CELL MATURATION; CONTROLLED STUDY; COTTON; ENZYME ACTIVITY; FLOWERING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OVULE; PLANT GENETICS; PRIORITY JOURNAL; REGULATORY MECHANISM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; WILD TYPE;

COTTON FIBER; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOME, PLANT; GOSSYPIUM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; MUTATION; PLANT PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

GOSSYPIUM HIRSUTUM;

EID: 78449234128     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.08.009     Document Type: Article

References (52)

1. Haigler C.H., Zhang D.H., Wilkerson C.G. Biotechnological improvement of cotton fibre maturity. Physiol. Plant. 2005, 124:285-294.
2. Yang S.S., et al. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fibre cell development in allotetraploid cotton. Plant J. 2006, 47:761-775.
3. Hovav R., et al. A majority of cotton genes are expressed in single-celled fibre. Planta 2008, 227:319-329.
4. J.J. Lee, A.W. Woodward, Z.J. Chen (2007) Gene expression changes and early events in cotton fibre development. Annual Bot. 100 (1984) 1391-1401.
5. Ruan Y.L., Chourey P.S. A fibreless seed mutation in cotton is associated with lack of fibre cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds. Plant Physiol. 1998, 118:399-406.
6. Li C.H., et al. Isolation of genes preferentially expressed in cotton fibres by cDNA filter arrays and RT-PCR. Plant Sci. 2002, 163:1113-1120.
7. Hülskamp M. Plant trichomes: a model for cell differentiation. Nat. Rev. Mol. Cell. Biol. 2004, 5:471-480.
8. Wang S., et al. Control of plant trichome development by a cotton fibre MYB gene. Plant Cell 2004, 16:2323-2334.
9. Ruan Y.L., Llewellyn D.J., Furbank R.T., Chourey P.S. The delayed initiation and slow elongation of fuzz-like short fibre cells in relation to altered patterns of sucrose synthase expression and plasmodesmata gating in a lintless mutant of cotton. J. Exp. Bot. 2005, 56:977-984.
10. Lee J.J., et al. Developmental and gene expression analyses of a cotton naked seed mutant. Planta 2006, 223:418-432.
11. Shangguan X.X., Xu B., Yu Z.X., Wang L.J., Chen X.Y. Promoter of a cotton fibre MYB gene functional in trichomes of Arabidopsis and glandular trichomes of tobacco. J. Exp. Bot. 2008, 59:3533-3542.
12. Humphries J.A., Walker A.R., Timmis J.N., Orford S.J. Two WD-repeat genes from cotton are functional homologues of the Arabidopsis thaliana TRANSPARENT TESTA GLABRA1 (TTG1) gene. Plant Mol. Biol. 2005, 57:67-81.
13. Oppenheimer O.G., Hermn P.L., Sivakumaran S., Esch J., Marks D.M. A myb gene required for leaf trichome differentiation in Arabidopsis is expressed in stipules. Cell 1991, 67:483-493.
14. Larkin J.C., Oppenheimer D.G., Lloyd A.M., Paparozzi E.T., Marks M.D. Roles of the GLABROUS1 and TRANSPARENT TESTA GLABRA genes in Arabidopsis trichome development. Plant Cell 1994, 6:1065-1076.
15. Payne T., Clement J., Arnold D., Lloyd A. Heterologous myb genes distinct from GL1 enhance trichome production when overexpressed in Nicotiana tabacum. Development 1999, 126:671-682.
16. Schellmann S., Hülskamp M. Epidermal differentiation: trichomes in Arabidopsis as a model system. Int. J. Dev. Biol. 2005, 49:579-584.
17. Arpat A.B., et al. Functional genomics of cell elongation in developing cotton fibres. Plant Mol. Biol. 2004, 54:911-929.
18. Wilkins T.A., Arpat A.B. The cotton fibre transcriptome. Physiol. Plant. 2005, 124:295-300.
19. 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 2006, 18:651-664.
20. Wu Y., Machado A.C., White R.G., Llewellyn D.J., Dennis E.S. Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol. 2006, 47:107-127.
21. Xu W.L., Wang X.L., Wang H., Li X.B. Molecular characterization and expression analysis of nine cotton GhEF1A genes encoding translation elongation factor 1A. Gene 2007, 389:27-35.
22. Ji S.J., et al. Isolation and analyses of genes preferentially expressed during early cotton fibre development by subtractive PCR and cDNA array. Nucleic Acids Res. 2003, 31:2534-2543.
23. Taliercio E.W., Boykin D. Analysis of gene expression in cotton fibre initials. BMC Plant Biol. 2007, 7:22.
24. Wu Y., et al. 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 2007, 226:1475-1490.
25. Li L., Wang X.L., Huang G.Q., Li X.B. Molecular characterization of cotton GhTUA9 gene specifically expressed in fibre and involved in cell elongation. J. Exp. Bot. 2007, 58:3227-3238.
26. Iandolino A., Nobuta K., da Silva F.G., Cook D.R., Meyers B.C. Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biol. 2008, 8:53.
27. Vizoso P., et al. Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality. BMC Genomics 2009, 10:423.
28. Hegedus Z., et al. Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol. Immunol. 2009, 46:2918-2930.
29. Kim H.J., Triplett B.A. Cotton fibre growth in planta and in vitro: models for plant cell elongation and cell wall biogenesis. Plant Physiol. 2001, 127:1361-1366.
30. Machado A., Wu Y., Yang Y., Llewellyn D.J., Dennis E.S. The MYB transcription factor GhMYB25 regulates early fibre and trichome development. Plant J. 2009, 59:52-62.
31. Loguercio L.L., Zhang J.Q., Wilkins T.A. Differential regulation of six novel MYB-domain genes defines two distinct expression patterns in allotetraploid cotton (Gossypium hirsutum L.). Mol. General Genetics 1999, 261:660-671.
32. Li X.B., Fan X.P., Wang X.L., Cai L., Yang W.C. The cotton ACTIN1 gene is functionally expressed in fibres and participates in fibre elongation. Plant Cell 2005, 17:859-875.
33. Preuss M.L., et al. A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibres. Plant Physiol. 2004, 136:3945-3955.
34. Huang Q.S., Wang H.Y., Gao P., Wang G.Y., Xia G.X. Cloning and characterization of a calcium dependent protein kinase gene associated with cotton fibre development. Plant Cell Rep. 2008, 27:1869-1875.
35. Notle K.D., Hendrix D.L., Radin J.W., Koch K.E. Sucrose synthase localization during initiation of seed development and trichome differentiation in cotton ovules. Plant Physiol. 1995, 109:1285-1293.
36. Ruan Y.L., Llewellyn D.J., Furbank R.T. Suppression of sucrose synthase gene expression represses cotton fibre cell initiation, elongation, and seed development. Plant Cell 2003, 15:952-964.
37. Xiao Y.H., et al. Gibberellin 20-oxidase promotes initiation and elongation of cotton fibres by regulating gibberellin synthesis. J. Plant Physiol. 2010, 167:829-837.
38. Wang H.H., et al. The essential role of GhPEL gene, encoding a pectate lyase, in cell wall loosening by depolymerization of the de-esterified pectin during fibre elongation in cotton. Plant Mol. Biol. 2010, 72:397-406.
39. Mei W., Qin Y., Song W., Li J., Zhu Y. Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fibre elongation. J. Genet. Genomics 2009, 36:141-150.
40. Michailidis G., Argirioua A., Darzentas N., Tsaftaris A. Analysis of xyloglucan endotransglycosylase hydrolase (XTH) genes from allotetraploid (Gossypium hirsutum) cotton and its diploid progenitors expressed during fibre elongation. J. Plant Physiol. 2008, 166:403-416.
41. Zhu Y.P., Xu K.X., Luo B., Wang J.W., Chen X.Y. An ATP-binding cassette transporter GhWBC1 from elongating cotton fibres. Plant Physiol. 2003, 133:580-588.
42. Xu Z., et al. Gene-rich islands for fibre development in the cotton genome. Genomics 2008, 92:173-183.
43. Pang M., et al. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fibre development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol. 2009, 10:R122.
44. Ruan M.B., Zhao Y.T., Meng Z.H., Wang X.J., Yang W.C. Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 2009, 94:263-268.
45. Kwak P.B., Wang Q.Q., Chen X.S., Qiu C.X., Yang Z.M. Enrichment of a set of microRNAs during the cotton fibre development. BMC Genomics 2009, 10:457.
46. Morrissy A.S., et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res. 2010, 19:1825-1835.
47. Rabinowicz P.D., et al. Differential methylation of genes and repeats in land plants. Genome Res. 2005, 15:1431-1440.
48. Pruitt R.E., Vielle-Calzada J.P., Ploense S.E., Grossniklaus U., Lolle S.J. FIDDLEHEAD, a gene required to suppress epidermal cell interactions in Arabidopsis, encodes a putative lipid biosynthetic enzyme. Proc. Natl Acad. Sci. USA 2000, 97:1311-1316.
49. Xue Y.J., Tao L., Yang Z.M. Aluminum-induced cell wall peroxidase activity and lignin synthesis are differentially regulated by jasmonate and nitric oxide. J. Agri Food Chem. 2008, 56:9676-9684.
50. Li H.B., et al. A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. New Phytol. 2007, 175:462-471.
51. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Res. 1997, 7:986-995.
52. Benjamini Y., Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 2001, 29:1165-1188.