Enrichment of a set of microRNAs during the cotton fiber development

BMC Genomics

Volumn 10, Issue , 2009, Pages 457-

  Kwak, Pieter B ^a   Wang, Qin Q ^a   Chen, Xu S ^b   Qiu, Cheng X ^a   Yang, Zhi M ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA;

ARTICLE; CELL ELONGATION; CELL TYPE; CONTROLLED STUDY; COTTON; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OVULE; PLANT DEVELOPMENT; PREDICTION; REGULATORY MECHANISM; RNA SEQUENCE; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; WILD TYPE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; PLANT GENOME;

GOSSYPIUM HIRSUTUM;

COTTON FIBER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOME, PLANT; GOSSYPIUM; MICRORNAS; RNA, PLANT; SEQUENCE ANALYSIS, RNA;

EID: 70350451757     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-457     Document Type: Article

References (48)

1. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 2002, 110:513-520. 10.1016/S0092-8674(02)00863-2, 12202040.
2. He L, Hannon GJ. Small RNAs with a big role in gene regulation. Nat Rev Genet 2004, 5:522-531. 10.1038/nrg1379, 15211354.
3. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36(Database issue):D154-D158. 2238936, 17991681.
4. Chapman EJ, Carrington JC. Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 2007, 8:884-896. 10.1038/nrg2179, 17943195.
5. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488. 10.1126/science.1138341, 17510325.
6. Hovav R, Udall JA, Hovav E, Rapp R, Flagel L, Wendel JF. A majority of cotton genes are expressed in single-celled fiber. Planta 2008, 227:319-29. 10.1007/s00425-007-0619-7, 17849148.
7. Kim HJ, Triplett BA. Cotton fiber growth in planta and in vitro: models for plant cell elongation and cell wall biogenesis. Plant Physiol 2001, 127:1361-1366. 10.1104/pp.010724, 1540163, 11743074.
8. Suo J, Liang X, Pu L, Zhang Y, Xue Y. Identification of GhMYB109 encoding a R2R3 MYB transcription factor that is expressed specifically in fiber initials and elongating fibers of cotton (Gossypium hirsutum L.). Biochim Biophys Acta 2003, 1630:25-34.
9. Wang S, Wang JW, Yu N, Li CH, Luo B, Gou JY, Wang LJ, Chen XY. Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 2004, 16:2323-2334. 10.1105/tpc.104.024844, 520936, 15316114.
10. Humphries JA, Walker AR, Timmis JN, Orford SJ. 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. 10.1007/s11103-004-6768-1, 15821869.
11. Ji SJ, Lu YC, Feng JX, Wei G, Li J, Shi YH, Fu Q, Liu D, Luo JC, Zhu YX. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array. Nucleic Acids Res 2003, 31:2534-2543. 10.1093/nar/gkg358, 156040, 12736302.
12. Yang SS, Cheung F, Lee JJ, Ha M, Wei NE, Sze SH, Stelly DM, Thaxton P, Triplett B, Town CD, Chen ZJ. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant J 2006, 47:761-775. 10.1111/j.1365-313X.2006.02829.x, 16889650.
13. Taliercio EW, Boykin D. Analysis of gene expression in cotton fiber initials. BMC Plant Biol 2007, 7:22. 10.1186/1471-2229-7-22, 1906782, 17506877.
14. Lee JJ, Hassan OS, Gao W, Wei NE, Kohel RJ, Chen XY, Payton P, Sze SH, Stelly DM, Chen ZJ. Developmental and gene expression analyses of a cotton naked seed mutant. Planta 2006, 223:418-32. 10.1007/s00425-005-0098-7, 16254724.
15. Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 2006, 18:651-64. 10.1105/tpc.105.040303, 1383640, 16461577.
16. Shangguan XX, Xu B, Yu ZX, Wang LJ, Chen XY. Promoter of a cotton fiber MYB gene functional in trichomes of Arabidopsis and glandular trichomes of tobacco. J Exp Bot 2008, 59:3533-3542. 10.1093/jxb/ern204, 2561158, 18711121.
17. Qiu CX, Xie FL, Zhu YY, Guo K, Huang SQ, Nie L, Yang ZM. Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 2007, 395:49-61. 10.1016/j.gene.2007.01.034, 17408884.
18. Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T, Cobb GP, Anderson TA. Identification of cotton microRNAs and their targets. Gene 2007, 397:26-37. 10.1016/j.gene.2007.03.020, 17574351.
19. Sunkar R, Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 2008, 8:37. 10.1186/1471-2229-8-37, 2358906, 18416839.
20. Zhang BH, Pan X, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J 2006, 46:243-259. 10.1111/j.1365-313X.2006.02697.x, 16623887.
21. Abdurakhmonov IY, Devor EJ, Buriev ZT, Huang L, Makamov A, Shermatov SE, Bozorov T, Kushanov FN, Mavlonov GT, Abdukarimov A. Small RNA regulation of ovule development in the cotton plant, G. hirsutum L. BMC Plant Biol 2008, 8:93. 10.1186/1471-2229-8-93, 2564936, 18793449.
22. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 2008, 18:571-584. 10.1101/gr.6897308, 2279245, 18323537.
23. Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 2006, 34:D731-D735. 10.1093/nar/gkj077, 1347440, 16381968.
24. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008, 18:957-964. 10.1101/gr.074740.107, 2413163, 18469162.
25. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. Criteria for annotation of plant microRNAs. Plant Cell 2008, 20:3186-90. 10.1105/tpc.108.064311, 19074682.
26. Gialvalis S, Seagull RW. Plant hormones alter fiber initiation in unfertilized cultured ovules of Gossypium hirsutum. J Cotton Sci 2001, 5:252-258.
27. Zhang TT, Pan JJ. Genetic analysis fuzzless-lintless mutant in Gossypium hirsutum L. JianSu J Agri Sci 1991, 7:13-16.
28. Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004, 16:2001-2019. 10.1105/tpc.104.022830, 519194, 15258262.
29. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 2005, 17:2186-2203. 10.1105/tpc.105.033456, 1182482, 15994906.
30. Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 2008, 133:116-127. 10.1016/j.cell.2008.02.034, 18342361.
31. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714. 10.1093/bioinformatics/btn025, 18227114.
32. Barozai MYK, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol Biochem 2008, 46:739-751. 10.1016/j.plaphy.2008.05.009, 18603441.
33. Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q. Cloning and characterization of microRNAs from wheat (Triticum aestivum. L.). Genome Biology 2007, 8:R96. 10.1186/gb-2007-8-6-r96, 2394755, 17543110.
34. Lu C, Kulkarni K, Souret FF, Valliappan RM, Tej SS, Poethig RS, Henderson RI, Jacobsen SE, Wang W, Green PJ, Meyers BC. RNA-dependent RNA polymerase-2 mutant microRNAs and other small RNAs enriched in the Arabidopsis. Genome Res 2006, 16:1276-1288. 10.1101/gr.5530106, 1581437, 16954541.
35. Reyes JL, Chua NH. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 2007, 49:592-606. 10.1111/j.1365-313X.2006.02980.x, 17217461.
36. Achard P, Herr A, Baulcombe DC, Harberd NP. Modulation of floral development by a gibberellin-regulated microRNA. Development 2004, 131:3357-3365. 10.1242/dev.01206, 15226253.
37. Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, Rodriguez R, Warthmann N, Allen E, Dezulian T, Huson D, Carrington JC, Weigel D. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev Cell 2007, 13:115-25. 10.1016/j.devcel.2007.04.012, 17609114.
38. Hsu C, An C, Saha S, Ma D, Jenkins JN, Scheffler B, Stelly DM. Molecular and SNP characterization of two genome specific transcription factor genes GhMyb8 and GhMyb10 in cotton species. Euphytica 2008, 159:259-273.
39. Kepinski S, Leyser O. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 2005, 435:446-451. 10.1038/nature03542, 15917798.
40. Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK. A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 2005, 15:2038-2043. 10.1016/j.cub.2005.10.016, 16303564.
41. Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su C. Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 2006, 18:412-421. 10.1105/tpc.105.038943, 1356548, 16387831.
42. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14:787-799. 10.1016/j.molcel.2004.05.027, 15200956.
43. Joshi PA, Stewart J, Graham ET. Ultrastructural localization of ATPase activity in cotton fiber development during elongation. Protoplasma 1988, 143:1-10.
44. Xiao Z, Tan K, Hu M, Liao P, Chen K, Luo M. Cloning and expression analysis of GhDET3, a vacuolar H+-ATPase subunit C gene, from cotton. J Genet Genomics 2008, 35:307-312. 10.1016/S1673-8527(08)60044-2, 18499075.
45. Sunkar R, Kapoor A, Zhu JK. Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell 2006, 18:2051-2065. 10.1105/tpc.106.041673, 1533975, 16861386.
46. Kim HJ, Kato N, Kim S, Triplett B. Cu/Zn superoxide dismutases in developing cotton fibers: evidence for an extracellular form. Planta 2008, 228:281-292. 10.1007/s00425-008-0734-0, 2440947, 18425534.
47. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288:911-940. 10.1006/jmbi.1999.2700, 10329189.
48. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev Cell 2005, 8:517-527. 10.1016/j.devcel.2005.01.018, 15809034.