Full Text:   <2458>

Suppl. Mater.: 

CLC number: S571.1

On-line Access: 2013-10-08

Received: 2013-01-04

Revision Accepted: 2013-04-01

Crosschecked: 2013-09-24

Cited: 14

Clicked: 3734

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2013 Vol.14 No.10 P.916-923


Identification of miRNAs and their targets in tea (Camellia sinensis)

Author(s):  Quan-wu Zhu, Yao-ping Luo

Affiliation(s):  Institute of Tea Science, Zhejiang University, Hangzhou 310058, China

Corresponding email(s):   ypluo@zju.edu.cn

Key Words:  MicroRNA (miRNA), Camellia sinensis, Tea, Gene ontology, PathwayThe online version of this article contains supplementary materials Data S1

Quan-wu Zhu, Yao-ping Luo. Identification of miRNAs and their targets in tea (Camellia sinensis)[J]. Journal of Zhejiang University Science B, 2013, 14(10): 916-923.

@article{title="Identification of miRNAs and their targets in tea (Camellia sinensis)",
author="Quan-wu Zhu, Yao-ping Luo",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Identification of miRNAs and their targets in tea (Camellia sinensis)
%A Quan-wu Zhu
%A Yao-ping Luo
%J Journal of Zhejiang University SCIENCE B
%V 14
%N 10
%P 916-923
%@ 1673-1581
%D 2013
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1300006

T1 - Identification of miRNAs and their targets in tea (Camellia sinensis)
A1 - Quan-wu Zhu
A1 - Yao-ping Luo
J0 - Journal of Zhejiang University Science B
VL - 14
IS - 10
SP - 916
EP - 923
%@ 1673-1581
Y1 - 2013
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1300006

MicroRNAs (miRNAs) are endogenous small RNAs playing a crucial role in plant growth and development, as well as stress responses. Among them, some are highly evolutionally conserved in the plant kingdom, this provide a powerful strategy for identifying miRNAs in a new species. tea (Camellia sinensis) is one of the most important commercial beverage crops in the world, but only a limited number of miRNAs have been identified. In the present study, a total of 14 new C. sinensis miRNAs were identified by expressed sequence tag (EST) analysis from 47452 available C. sinensis ESTs. These miRNAs potentially target 51 mRNAs, which can act as transcription factors, and participate in stress response, transmembrane transport, and signal transduction. Analysis of gene ontology (GO), based on these targets, suggested that 37 biological processes were involved, such as oxidation-reduction process, stress response, and transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis inferred that the identified miRNAs took part in 13 metabolic networks. Our study will help further understanding of the essential roles of miRNAs in C. sinensis growth and development, and stress response.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res., 25(17):3389-3402.

[2]Bartel, D.P., 2004. microRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2):281-297.

[3]Carra, A., Mica, E., Gambino, G., Pindo, M., Moser, C., Pe, M.E., Schubert, A., 2009. Cloning and characterization of small non-coding RNAs from grape. Plant J., 59(5): 750-763.

[4]Chen, X.M., 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303(5666):2022-2025.

[5]Chen, X., Zhang, Z., Liu, D., Zhang, K., Li, A., Mao, L., 2010. Squamosa promoter-binding protein-like transcription factors: star players for plant growth and development. J. Integr. Plant Biol., 52(11):946-951.

[6]Conesa, A., Götz, S., 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genom., 2008:619832.

[7]Conesa, A., Götz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., Robles, M., 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3674-3676.

[8]Das, A., Mondal, T.K., 2010. Computational identification of conserved microRNAs and their targets in tea (Camellia sinensis). Am. J. Plant Sci., 01(02):77-86.

[9]Ding, D., Zhang, L., Wang, H., Liu, Z., Zhang, Z., Zheng, Y., 2009. Differential expression of miRNAs in response to salt stress in maize roots. Ann. Bot., 103(1):29-38.

[10]Dong, Q.H., Han, J., Yu, H.P., Wang, C., Zhao, M.Z., Liu, H., Ge, A.J., Fang, J.G., 2012. Computational identification of microRNAs in strawberry expressed sequence tags and validation of their precise sequences by miR-RACE. J. Heredity, 103(2):268-277.

[11]Frazier, T.P., Zhang, B., 2011. Identification of Plant MicroRNAs Using Expressed Sequence Tag Analysis. In: Pereira, A. (Ed.), Plant Reverse Genetics. Humana Press, New York, p.13-25.

[12]Frazier, T.P., Xie, F., Freistaedter, A., Burklew, C.E., Zhang, B., 2010. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta, 232(6):1289-1308.

[13]Gou, J.Y., Felippes, F.F., Liu, C.J., Weigel, D., Wang, J.W., 2011. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell, 23(4):1512-1522.

[14]Guo, H.S., Xie, Q., Fei, J.F., Chua, N.H., 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell, 17(5):1376-1386.

[15]He, L., Hannon, G.J., 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 5(7):522-531.

[16]Heo, J.O., Chang, K.S., Kim, I.A., Lee, M.H., Lee, S.A., Song, S.K., Lee, M.M., Lim, J., 2011. Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root. PNAS, 108(5):2166-2171.

[17]Juarez, M.T., Kui, J.S., Thomas, J., Heller, B.A., Timmermans, M.C.P., 2004. MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature, 428(6978): 84-88.

[18]Kanehisa, M., Goto, S., 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucl. Acids Res., 28(1):27-30.

[19]Kozomara, A., Griffiths-Jones, S., 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucl. Acids Res., 39:D152-D157.

[20]Li, B., Qin, Y., Duan, H., Yin, W., Xia, X., 2011. Genome-wide characterization of new and drought stress responsive microRNAs in populus euphratica. J. Exp. Bot., 62(11):3765-3779.

[21]Mallory, A.C., Reinhart, B.J., Jones-Rhoades, M.W., Tang, G.L., Zamore, P.D., Barton, M.K., Bartel, D.P., 2004. MicroRNA control of phabulosa in leaf development: importance of pairing to the microRNA 5′ region. EMBO J., 23(16):3356-3364.

[22]Mohanpuria, P., Yadav, S.K., 2012. Characterization of novel small RNAs from tea (Camellia sinensis L.). Mol. Biol. Rep., 39(4):3977-3986.

[23]Moxon, S., Jing, R.C., Szittya, G., Schwach, F., Pilcher, R.L.R., Moulton, V., Dalmay, T., 2008. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res., 18(10):1602-1609.

[24]Palatnik, J.F., Allen, E., Wu, X.L., Schommer, C., Schwab, R., Carrington, J.C., Weigel, D., 2003. Control of leaf morphogenesis by microRNAs. Nature, 425(6955):257-263.

[25]Prabu, G.R., Mandal, A.K., 2010. Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genom. Prot. Bioinf., 8(2):113-121.

[26]Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., Bartel, D.P., 2002. MicroRNAs in plants. Genes Dev., 16(13):1616-1626.

[27]Rogers, P.J., Smith, J.E., Heatherley, S.V., Pleydell-Pearce, C.W., 2008. Time for tea: mood, blood pressure and cognitive performance effects of caffeine and theanine administered alone and together. Psychopharmacology, 195(4):569-577.

[28]Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., Weigel, D., 2005. Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 8(4):517-527.

[29]Shi, C.Y., Yang, H., Wei, C.L., Yu, O., Zhang, Z.Z., Jiang, C.J., Sun, J., Li, Y.Y., Chen, Q., Xia, T., et al., 2011. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genom., 12:131.

[30]Song, C., Jia, Q., Fang, J., Li, F., Wang, C., Zhang, Z., 2010. Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biol., 12(6):927-934.

[31]Sunkar, R., Chinnusamy, V., Zhu, J., Zhu, J.K., 2007. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci., 12(7):301-309.

[32]Sunkar, R., Li, Y.F., Jagadeeswaran, G., 2012. Functions of microRNAs in plant stress responses. Trends Plant Sci. 17(4):196-203.

[33]Thiebaut, F., Rojas, C.A., Almeida, K.L., Grativol, C., Domiciano, G.C., Lamb, C.R.C., de Almeida Engler, J., Hemerly, A.S., Ferreira, P.C.G., 2012. Regulation of miR319 during cold stress in sugarcane. Plant Cell Env., 35(3):502-512.

[34]Wang, J.W., Czech, B., Weigel, D., 2009. miR156-regulated spl transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell, 138(4):738-749.

[35]Wang, X.J., Reyes, J.L., Chua, N.H., Gaasterland, T., 2004. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol., 5(9):R65

[36]Williams, L., Grigg, S.P., Xie, M.T., Christensen, S., Fletcher, J.C., 2005. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development, 132(16):3657-3668.

[37]Wu, G., Park, M.Y., Conway, S.R., Wang, J.W., Weigel, D., Poethig, R.S., 2009. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell, 138(4):750-759.

[38]Xie, F., Frazier, T.P., Zhang, B., 2010. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta, 232(2):417-434.

[39]Xie, F., Frazier, T.P., Zhang, B., 2011. Identification, characterization and expression analysis of microRNAs and their targets in the potato (Solanum tuberosum). Gene, 473(1):8-22.

[40]Xie, F.L., Huang, S.Q., Guo, K., Xiang, A.L., Zhu, Y.Y., Nie, L., Yang, Z.M., 2007. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett., 581(7):1464-1474.

[41]Yin, Z., Li, C., Han, X., Shen, F., 2008. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414(1-2):60-66.

[42]Yu, H., Song, C., Jia, Q., Wang, C., Li, F., Nicholas, K.K., Zhang, X., Fang, J., 2011. Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE. Physiol. Plant, 141(1):56-70.

[43]Zhang, B.H., Pan, X.P., Wang, Q.L., Cobb, G.P., Anderson, T.A., 2005. Identification and characterization of new plant microRNAs using EST analysis. Cell Res., 15(5):336-360.

[44]Zhang, B., Pan, X., Cannon, C.H., Cobb, G.P., Anderson, T.A., 2006a. Conservation and divergence of plant microRNA genes. Plant J., 46(2):243-259.

[45]Zhang, B.H., Pan, X.P., Cox, S.B., Cobb, G.P., Anderson, T.A., 2006b. Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci., 63(2):246-254.

[46]Zhang, B., Pan, X., Stellwag, E.J., 2008. Identification of soybean microRNAs and their targets. Planta, 229(1):161-182.

[47]Zhang, J., Xu, Y., Huan, Q., Chong, K., 2009. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genom., 10:449.

[48]Zhao, M., Tai, H., Sun, S., Zhang, F., Xu, Y., Li, W.X., 2012. Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency. PLoS One, 7(1): e29669.

[49]Zhou, Z.S., Huang, S.Q., Yang, Z.M., 2008. Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula. Biochem. Biophys. Res. Commun., 374(3):538-542.

[50]Zuker, M., 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res., 31(13):3406-3415.

Open peer comments: Debate/Discuss/Question/Opinion


Please provide your name, email address and a comment

Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE