Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G. raimondii Genome

Qin Li; Xiang Jin; Yu-Xian Zhu

doi:10.1016/j.jgg.2012.04.008

Volume 39 Issue 7

Jul. 2012

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2012 > 39(7): 351-360

PDF( 1289 KB)

Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G. raimondii Genome

doi: 10.1016/j.jgg.2012.04.008

a
The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
b
National Center for Plant Gene Research (Beijing), Beijing 100101, China

More Information

Corresponding author: E-mail address: zhuyx2@pku.edu.cn (Yu-Xian Zhu)
Received Date: 2012-02-13
Accepted Date: 2012-04-25
Rev Recd Date: 2012-04-25

Available Online: 2012-05-17

Publish Date: 2012-07-20

Abstract

Abstract

The plant genome possesses a large number of microRNAs (miRNAs) mainly 21–24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ∼10million non-coding RNAs (ncRNAs) derived from fiber tissue of the allotetraploid cotton (Gossypium hirsutum) 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D₅ genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10–20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.
- Cotton,
- Genome,
- Micro RNA,
- Deep sequencing,
- Microarray

FullText(HTML)

References(45)

References

[1]	Allen, E., Xie, Z., Gustafson, A.M. et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants Cell, 121 (2005),pp. 207-221
[2]	Ambros, V., Bartel, B., Bartel, D.P. et al. A uniform system for microRNA annotation RNA, 9 (2003),pp. 277-279
[3]	Aukerman, M.J., Sakai, H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes Plant Cell, 15 (2003),pp. 2730-2741
[4]	Bartel, D. MicroRNAs: genomics, biogenesis, mechanism, and function Cell, 116 (2004),pp. 281-297
[5]	Baulcombe, D. RNA silencing in plants Nature, 431 (2004),pp. 356-363
[6]	Blanc, G., Wolfe, K.H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes Plant Cell, 16 (2004),pp. 1667-1678
[7]	Bowers, J.E., Chapman, B.A., Rong, J. et al. Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events Nature, 422 (2003),pp. 433-438
[8]	Chapman, E.J., Carrington, J.C. Specialization and evolution of endogenous small RNA pathways Nat. Rev. Genet., 8 (2007),pp. 884-896
[9]	Chen, X. Science, 303 (2004),pp. 2022-2025
[10]	Chen, Z.J., Scheffler, B.E., Dennis, E. et al. Plant Physiol., 145 (2007),pp. 1303-1310
[11]	Chuck, G., Cigan, A.M., Saeteurn, K. et al. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA Nat. Genet., 39 (2007),pp. 544-549
[12]	Elemento, O., Gascuel, O., Lefranc, M.P. Reconstructing the duplication history of tandemly repeated genes Mol. Biol. Evol., 19 (2002),pp. 278-288
[13]	Fawcett, J.A., Maere, S., Van de Peer, Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 5737-5742
[14]	Griffiths-Jones, S., Saini, H.K., van Dongen, S. et al. miRBase: tools for microRNA genomics Nucleic Acids Res., 36 (2008),pp. D154-D158
[15]	Hendrix, B., Stewart, J.M. Ann. Bot., 95 (2005),pp. 789-797
[16]	Ji, S.-J., Lu, Y.-C., Feng, J.-X. et al. Isolation and analyses of genes preferentially expressed during early cotton fiber development by subtractive PCR and cDNA array Nucleic Acids Res., 31 (2003),pp. 2534-2543
[17]	Jones-Rhoades, M.W., Bartel, D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA Mol. Cell, 14 (2004),pp. 787-799
[18]	Kang, B.-H., Busse, J.S., Bednarek, S.Y. Plant Cell, 15 (2003),pp. 899-913
[19]	Kim, H.J., Triplett, B.A. Plant Physiol., 127 (2001),pp. 1361-1366
[20]	Kurihara, Y., Watanabe, Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 12753-12758
[21]	Kwak, P.B., Wang, Q.-Q., Chen, X.-S. et al. Enrichment of a set of microRNAs during the cotton fiber development BMC Genomics, 10 (2009),p. 457
[22]	Lewis, B.P., Shih, I.-h., Jones-Rhoades, M.W. et al. Prediction of mammalian microRNA targets Cell, 115 (2003),pp. 787-798
[23]	Li, Y., Liu, X., Huang, L. et al. Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in Archaea J. Genet. Genomics, 37 (2010),pp. 493-503
[24]	Llave, C., Xie, Z., Kasschau, K.D. et al. Science, 297 (2002),pp. 2053-2056
[25]	Lu, C. Elucidation of the small RNA component of the transcriptome Science, 309 (2005),pp. 1567-1569
[26]	Mei, W.-Q., Qin, Y.-M., Song, W.-Q. et al. J. Genet. Genomics, 36 (2009),pp. 141-150
[27]	Meyers, B.C., Axtell, M.J., Bartel, B. et al. Criteria for annotation of plant microRNAs Plant Cell, 20 (2008),pp. 3186-3190
[28]	Mi, S., Cai, T., Hu, Y. et al. Cell, 133 (2008),pp. 116-127
[29]	Miao, W., Wang, X., Song, C. et al. J. Exp. Bot., 61 (2010),pp. 4263-4275
[30]	Pang, C.-Y., Wang, H., Pang, Y. et al. Mol. Cell. Proteomics, 9 (2010),pp. 2019-2033
[31]	Pang, M., Woodward, A.W., Agarwal, V. et al. Genome Biol., 10 (2009),p. R122
[32]	Pasapula, V., Shen, G., Kuppu, S. et al. Plant Biotechnol. J., 9 (2011),pp. 88-99
[33]	Paterson, A.H., Bowers, J.E., Chapman, B.A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 9903-9908
[34]	Qin, Y.-M., Zhu, Y.-X. How cotton fibers elongate: a tale of linear cell-growth mode Curr. Opin. Plant Biol., 14 (2011),pp. 106-111
[35]	Qin, Y.-M., Hu, C.-Y., Pang, Y. et al. Plant Cell, 19 (2007),pp. 3692-3704
[36]	Qiu, C.-X., Xie, F.-L., Zhu, Y.-Y. et al. Gene, 395 (2007),pp. 49-61
[37]	Rajagopalan, R., Vaucheret, H., Trejo, J. et al. Genes Dev., 20 (2006),pp. 3407-3425
[38]	Saeed, A.I., Bhagabati, N.K., Braisted, J.C. et al. TM4 microarray software suite Methods Enzymol., 411 (2006),pp. 134-193
[39]	Senchina, D.S., Alvarez, I., Cronn, R.C. et al. Mol. Biol. Evol., 20 (2003),pp. 633-643
[40]	Shi, Y.-H., Zhu, S.-W., Mao, X.-Z. et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation Plant Cell, 18 (2006),pp. 651-664
[41]	Wang, Y., Itaya, A., Zhong, X. et al. Plant Cell, 23 (2011),pp. 3185-3203
[42]	Wang, Z.-M., Xue, W., Dong, C.-J. et al. A comparative miRNAome analysis reveals seven fiber initiation-related and 36 novel miRNAs in developing cotton ovules Mol. Plant (2011)
[43]	Wendel, J., Albert, V. System. Bot., 17 (1992),pp. 115-143
[44]	Wu, Z., Soliman, K.M., Bolton, J.J. et al. Identification of differentially expressed genes associated with cotton fiber development in a chromosomal substitution line (CS-B22sh) Funct. Integr. Genomics, 8 (2008),pp. 165-174
[45]	Zhang, B., Wang, Q., Wang, K. et al. Identification of cotton microRNAs and their targets Gene, 397 (2007),pp. 26-37