MicroRNAs in cotton: an open world needs more exploration
Tóm tắt
This paper reviews the progress and current problems in the field of cotton microRNAs.
Cotton is not only one of the most important crops in terms of fiber usage and economic value, but also a model species for investigating cell wall and cellulose biosynthesis as well plant polyploidization. Compared with model plant species, such as Arabidopsis and rice, the research on cotton microRNAs (miRNAs) is lagging, although great progress has been made in the past decade. Since the first reports on identifying miRNAs in cotton in 2007, hundreds of miRNAs have been identified using an in silico comparative genome-based approach and direct cloning. Next-generation deep sequencing has opened the door for cotton miRNA research. In cotton, miRNAs are associated with many biological and metabolic processes, including fiber initiation and development, floral development, embryogenesis, and response to biotic and abiotic stresses. However, the majority of current research is focused on miRNA identification. Although several targets have been predicted using computational approaches and degradome sequencing, more functional studies should be performed in the next couple of years to elucidate the roles of miRNAs in cotton fiber development and response to different environmental stresses using transgenic technology. This paper reviews the history, identification, and function of cotton miRNAs as well as future directions for this research.
Tài liệu tham khảo
Abdurakhmonov IY, Devor EJ, Buriev ZT, Huang LY, Makamov A, Shermatov SE, Bozorov T, Kushanov FN, Mavlonov GT, Abdukarimov A (2008) Small RNA regulation of ovule development in the cotton plant G. hirsutum L. BMC Plant Biol. doi:10.1186/1471-2229-8-93
Axtell MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17(6):1658–1673. doi:10.1105/tpc.105.032185
Barozai MYK, Irfan M, Yousaf R, Ali I, Qaisar U, Maqbool A, Zahoor M, Rashid B, Hussnain T, Riazuddin S (2008) Identification of micro-RNAs in cotton. Plant Physiol Biochem 46(8–9):739–751. doi:10.1016/j.plaphy.2008.05.009
Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38(20):6883–6894. doi:10.1093/nar/gkq590
Chen X (2005) microRNA biogenesis and function in plants. FEBS Letters 579(26, Sp. Iss. SI):5923–5931. doi:10.1016/j.febslet.2005.07.071
Chen X, Gao W, Zhang J, Zhang X, Lin Z (2013) Linkage mapping and expression analysis of miRNAs and their target genes during fiber development in cotton. BMC Genom 14:706. doi:10.1186/1471-2164-14-706
Gong L, Kakrana A, Arikit S, Meyers BC, Wendel JF (2013) Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol Evol 5(12):2449–2459. doi:10.1093/gbe/evt196
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Research 36(Sp. Iss. SI):D154–D158. doi:10.1093/nar/gkm952
Gu ZH, Huang CJ, Li FF, Zhou XP (2014) A versatile system for functional analysis of genes and microRNAs in cotton. Plant Biotechnol J 12(5):638–649. doi:10.1111/pbi.12169
Guan X, Pang M, Nah G, Shi X, Ye W, Stelly DM, Chen ZJ (2014) miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nat Commun. doi:10.1038/ncomms4050
He Q, Zhu S, Zhang B (2014) MicroRNA–target gene responses to lead-induced stress in cotton (Gossypium hirsutum L.). Funct Integr Genomics 14(3):507–515. doi:10.1007/s10142-014-0378-z
Kim VN, Nam J-W (2006) Genomics of microRNA. Trends Genet 22(3):165–173. doi:10.1016/j.tig.2006.01.003
Kwak PB, Wang QQ, Chen XS, Qiu CX, Yang ZM (2009) Enrichment of a set of microRNAs during the cotton fiber development. BMC Genom. doi:10.1186/1471-2164-10-457
Li Q, Jin X, Zhu Y-X (2012) Identification and analyses of miRNA genes in allotetraploid Gossypium hirsutum fiber cells based on the sequenced diploid G-raimondii genome. J Genet Genomics 39(7):351–360. doi:10.1016/j.jgg.2012.04.008
Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, Li Q, Ma Z, Lu C, Zou C, Chen W, Liang X, Shang H, Liu W, Shi C, Xiao G, Gou C, Ye W, Xu X, Zhang X, Wei H, Li Z, Zhang G, Wang J, Liu K, Kohel RJ, Percy RG, Yu JZ, Zhu Y-X, Wang J, Yu S (2014) Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 46(6):567–572. doi:10.1038/ng.2987
Liu N, Tu L, Tang W, Gao W, Lindsey K, Zhang X (2014) Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers of Gossypium barbadense. The Plant Journal:n/a-n/a. doi:10.1111/tpj.12636
Ma J, Guo TL, Wang QL, Wang KB, Sun RR, Zhang BH (2015) Expression profiles of miRNAs in Gossypium raimondii. J Zhejiang Univ Sci B 16(4):306–313. doi:10.1631/jzus.B1400277
Pang M, Woodward A, Agarwal V, Guan X, Ha M, Ramachandran V, Chen X, Triplett B, Stelly D, Chen ZJ (2009) Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol 10(11):R122
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, ur Rahman M, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423–427. doi:10.1038/nature11798
Peng Z, He S, Gong W, Sun J, Pan Z, Xu F, Lu Y, Du X (2014) Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. BMC Genom 15(1):760
Qiu CX, Xie FL, Zhu YY, Guo K, Huang SQ, Nie L, Yang ZM (2007) Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395(1–2):49–61. doi:10.1016/j.gene.2007.01.034
Romanel E, Silva TF, Correa RL, Farineli L, Hawkins JS, Schrago CE, Vaslin MF (2012) Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during cotton leafroll dwarf polerovirus (CLRDV) infection. Plant Mol Biol 80:443–460. doi:10.1007/s11103-012-9959-1
Sun RR, Wang QL, Ma J, He QL, Zhang BH (2014) Differentiated expression of microRNAs may regulate genotype-dependent traits in cotton. Gene 547(2):233–238. doi:10.1016/j.gene.2014.06.052
Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4):669–687. doi:10.1016/j.cell.2009.01.046
Wang M, Wang QL, Wang BM (2012a) Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS One. doi:10.1371/journal.pone.0033696
Wang Z-M, Xue W, Dong C-J, Jin L-G, Bian S-M, Wang C, Wu X-Y, Liu J-Y (2012b) A comparative miRNAome analysis reveals seven fiber initiation-related and 36 novel miRNAs in developing cotton ovules. Mol Plant 5(4):889–900. doi:10.1093/mp/ssr094
Wang M, Wang QL, Zhang BH (2013) Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene 530(1):26–32. doi:10.1016/j.gene.2013.08.009
Wei MM, Wei HL, Wu M, Song MZ, Zhang JF, Yu JW, Fan SL, Yu SX (2013) Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton. BMC Plant Biol. doi:10.1186/1471-2229-13-66
Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38(3):465–475. doi:10.1016/j.molcel.2010.03.008
Xie FL, Zhang BH (2015) MicroRNA evolution and expression analysis in polyploidized cotton genome. Plant Biotechnol J 13:404–417. doi:10.1111/pbi.12295
Xie Z, Kasschau KD, Carrington JC (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol 13(9):784–789. doi:10.1016/S0960-9822(03)00281-1
Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of arabidopsis miRNA genes. Plant Physiol (Rockville) 138(4):2145–2154. doi:10.1104/pp.105.062943
Xie FL, Jones DC, Wang QL, Sun RR, Zhang BH (2015a) Small RNA sequencing identifies miRNA roles in ovule and fiber development. Plant Biotechnol J 13:338–352. doi:10.1111/pbi.12296
Xie FL, Wang QL, Sun RR, Zhang BH (2015b) Deep sequencing deciphers important miRNA roles in response to drought and salinity stress in cotton. J Exp Bot 66:789–804. doi:10.1093/jxb/eru437
Xie FL, Wang QL, Zhang BH (2015c) Global microRNA modification in cotton (Gossypium hirsutum L.). Plant Biotechnol J. doi:10.1111/pbi.12271
Xue W, Wang Z, Du M, Liu Y, Liu J-Y (2013a) Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells. BMC Genomics 14:629. doi:10.1186/1471-2164-14-629
Xue W, Wang ZM, Du MJ, Liu YD, Liu JY (2013b) Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells. BMC Genomics. doi:10.1186/1471-2164-14-629
Yang X, Wang L, Yuan D, Lindsey K, Zhang X (2013) Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot 64:1521–1536. doi:10.1093/jxb/ert013
Yin ZJ, Li Y, Han XL, Shen FF (2012a) Genome-wide profiling of miRNAs and other small non-coding RNAs in the verticillium dahliae-Inoculated cotton roots. PLoS One. doi:10.1371/journal.pone.0035765
Yin ZJ, Li Y, Yu JW, Liu YD, Li CH, Han XL, Shen FF (2012b) Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity. Mol Biol Rep 39(4):4961–4970. doi:10.1007/s11033-011-1292-2
Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot. doi:10.1093/jxb/erv013
Zhang BH, Pan XP (2009) Expression of MicroRNAs in cotton. Mol Biotechnol 42(3):269–274. doi:10.1007/s12033-009-9163-y
Zhang B, Wang Q (2015) MicroRNA-based biotechnology for plant improvement. J Cell Physiol 230:1–15. doi:10.1002/jcp.24685.10.1002/jcp.24685
Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15(5):336–360. doi:10.1038/sj.cr.7290302
Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006a) Conservation and divergence of plant microRNA genes. Plant J 46(2):243–259. doi:10.1111/j.1365-313X.2006.02697.X
Zhang BH, Pan XP, Cobb GP, Anderson TA (2006b) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289(1):3–16. doi:10.1016/j.ydbio.2005.10.036
Zhang BH, Wang QL, Wang KB, Pan XP, Liu F, Guo TL, Cobb GP, Anderson TA (2007) Identification of cotton microRNAs and their targets. Gene 397(1–2):26–37. doi:10.1016/j.gene.2007.03.020
Zhang XH, Zou Z, Gong PJ, Zhang JH, Ziaf K, Li HX, Xiao FM, Ye ZB (2011) Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnol Lett 33(2):403–409. doi:10.1007/s10529-010-0436-0
Zhang H, Wan Q, Ye W, Lv Y, Wu H, Zhang T (2013) Genome-wide analysis of small RNA and novel microRNA discovery during fiber and seed initial development in Gossypium hirsutum. L. PLoS One 8(7):e69743. doi:10.1371/journal.pone.0069743
Zhu QH, Fan LJ, Liu Y, Xu H, Llewellyn D, Wilson I (2013) miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. PLoS One. doi:10.1371/journal.pone.0084390