Full Text:   <2042>

Summary:  <1341>

Suppl. Mater.: 

CLC number: Q291

On-line Access: 2015-12-04

Received: 2015-06-21

Revision Accepted: 2015-11-07

Crosschecked: 2015-11-16

Cited: 1

Clicked: 3532

Citations:  Bibtex RefMan EndNote GB/T7714


Hong-chang Liu


-   Go to

Article info.
Open peer comments

Journal of Zhejiang University SCIENCE B 2015 Vol.16 No.12 P.1027-1041


Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate

Author(s):  Hong-chang Liu, Wei Wu, Kai Hou, Jun-wen Chen, Zhi Zhao

Affiliation(s):  College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; more

Corresponding email(s):   ewuwei@sicau.edu.cn

Key Words:  Polygonum multiflorum Thunb., Methyl jasmonate, Transcriptome change, Differentially expressed genes

Hong-chang Liu, Wei Wu, Kai Hou, Jun-wen Chen, Zhi Zhao. Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate[J]. Journal of Zhejiang University Science B, 2015, 16(12): 1027-1041.

@article{title="Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate",
author="Hong-chang Liu, Wei Wu, Kai Hou, Jun-wen Chen, Zhi Zhao",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate
%A Hong-chang Liu
%A Wei Wu
%A Kai Hou
%A Jun-wen Chen
%A Zhi Zhao
%J Journal of Zhejiang University SCIENCE B
%V 16
%N 12
%P 1027-1041
%@ 1673-1581
%D 2015
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1500150

T1 - Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate
A1 - Hong-chang Liu
A1 - Wei Wu
A1 - Kai Hou
A1 - Jun-wen Chen
A1 - Zhi Zhao
J0 - Journal of Zhejiang University Science B
VL - 16
IS - 12
SP - 1027
EP - 1041
%@ 1673-1581
Y1 - 2015
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1500150

Transcriptome profiling has been widely used to analyze transcriptomic variation in plants subjected to abiotic or biotic stresses. Although gene expression changes induced by methyl jasmonate (MeJA) have been profiled in several plant species, no information is available on the MeJA-triggered transcriptome response of Polygonum multiflorum Thunb., a species with highly valuable medicinal properties. In this study, we used transcriptome profiling to investigate transcriptome changes in roots of P. multiflorum seedlings subjected to a 0.25 mmol/L-MeJA root-irrigation treatment. A total of 18 677 differentially expressed genes (DEGs) were induced by MeJA treatment, of which 4535 were up-regulated and 14 142 were down-regulated compared with controls. These DEGs were associated with 125 metabolic pathways. In addition to various common primary and secondary metabolic pathways, several secondary metabolic pathways related to components with significant pharmacological effects were enriched by MeJA, including arachidonic acid metabolism, linoleic acid metabolism, and stilbenoid biosynthesis. The MeJA-induced transcriptome changes uncovered in this study provide a solid foundation for future study of functional genes controlling effective components in secondary metabolic pathways of P. multiflorum.


目的:研究外源茉莉酸甲酯(MeJA)处理对中药何首乌(Polygonum multiflorum)根转录组的影响,分析在外源MeJA刺激下何首乌根各代谢途径中差异表达基因的变化,为寻找影响何首乌根主要药效成分合成的关键酶基因奠定基础。
方法:将何首乌植株分为对照组(Hoagland营养液灌根)和实验组(含0.25 mmol/L MeJA的Hoagland营养液灌根)。灌根处理26 h后,分别提取对照组和实验组根中的总RNA,利用新一代测序技术分析对照组和实验组根的转录组变化并进行测序。同时,利用美国国家生物技术信息中心(NCBI)的蛋白质数据库和基因数据库信息,对所测cDNA序列进行基因功能注释和代谢途径归类,寻找MeJA刺激下何首乌根各条代谢途径中的差异表达基因。
结论:外源MeJA刺激处理可影响中药何首乌根转录组的表达变化(表S1)。与对照相比,外源MeJA处理可导致何首乌根中4535个基因上调,14 142个基因下调变化,并分别在125个代谢途径中富集(表1)。代谢途径差异表达基因分析的结果表明,可在相应代谢途径中找到影响何首乌某些主要药效成分合成的关键酶基因(图2)。差异表达基因的代谢途径归类分析结果提示今后可对何首乌根各代谢途径中的关键酶基因分别进行研究(表1)。综上所述,利用外源MeJA处理后进行转录组测序对寻找何首乌中主要有效成份合成的关键酶基因有重要价值。


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


[1]Audic, S., Claverie, J.M., 1997. The significance of digital gene expression profiles. Genome Res., 10(7):986-995.

[2]Benjamini, Y., Drai, D., Elmer, G., et al., 2001. Controlling the false discovery rate in behavior genetics research. Behav. Brain Res., 125(1-2):279-284.

[3]Chang, L.L., Zhang, Y.T., Wang, G.X., et al., 2013. The effects of exogenous methyl jasmonate on FaNES1 gene expression and the biosynthesis of volatile terpenes in strawberry (Fragaria X ananassa Duch.) fruit. J. Hortic. Sci. Biotech., 88(4):393-398.

[4]Conesa, A., Gotz, S., 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics, 2008:619832.

[5]Conesa, A., Gotz, S., Garcia-Gomez, J.M., et al., 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3674-3676.

[6]Diallo, A.O., Agharbaoui, Z., Badawi, M.A., et al., 2014. Transcriptome analysis of an mvp mutant reveals important changes in global gene expression and a role for methyl jasmonate in vernalization and flowering in wheat. J. Exp. Bot., 65(9):2271-2286.

[7]Gaige, A.R., Ayella, A., Shuai, B., 2010. Methyl jasmonate and ethylene induce partial resistance in Medicago truncatula against the charcoal rot pathogen Macrophomina phaseolina. Physiol. Mol. Plant Pathol., 74(5-6):412-418.

[8]Grabherr, M.G., Haas, B.J., Yassour, M., et al., 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol., 29(7):644-652.

[9]Han, J.L., Li, Z.Q., Liu, B.Y., et al., 2007. Metabolic engineering of terpenoids in plants. Chin. J. Biotech., 23(4):561-569.

[10]Hoagland, D.R., Arnon, D.I., 1950. The water-culture method for growing plants without soil. Calif. Agric. Exp. Sta. Circular, 347:32.

[11]Huggett, J., Dheda, K., Bustin, S., et al., 2005. Real-time RT-PCR normalization; strategies and considerations. Genes Immun., 6(4):279-284.

[12]Iseli, C., Jonqeneel, C.V., Bucher, P., 1999. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. International Conference on Intelligent Systems for Molecular Biology, p.138-148.

[13]Jeandet, P., Douillet-Breuil, A.C., Bessis, R., et al., 2002. Phytoalexins from the Vitaceae: biosynthesis, phytoalexin gene expression in transgenic plants, antifungal activity, and metabolism. J. Agric. Food Chem., 50(10):2731-2741.

[14]Ku, K.M., Juvik, J.A., 2013. Environmental stress and methyl jasmonate-mediated changes in flavonoid concentrations and antioxidant activity in Broccoli Florets and Kale leaf tissues. Hortscience, 48(8):996-1002.

[15]Li, R.Q., Zhu, H.M., Ruan, J., et al., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20(2):265-272.

[16]Li, Y.F., Nie, Y.F., Zhang, Z.H., et al., 2014. Comparative proteomic analysis of methyl jasmonate induced defense responses in different rice cultivars. Proteomics, 14(9):1088-1101.

[17]Lin, L.C., Nalawade, S.M., Mulabagal, V., et al., 2003. Micropropagation of Polygonum multiflorum Thunb. and quantitative analysis of the anthraquinones emodin and physcion formed in vitro propagated shoots and plants. Biol. Pharm. Bull., 26(10):1467-1471.

[18]Lin, L.F., Ni, B.R., Lin, H.M., et al., 2015. Traditional usages, botany, phytochemistry, pharmacology and toxicology of Polygonum multiflorum Thunb.: a review. J. Ethnopharmacol., 159:158-183.

[19]Liu, H.C., Wu, W., Hou, K., et al., 2015. Deep sequencing reveals transcriptome re-programming of Polygonum multiflorum Thunb. roots to the elicitation with methyl jasmonate. Mol. Genet. Gemomics, in press.

[20]Livak, K.J., Schmittgen, T.D., 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−∆∆CT method. Methods, 25(4):402-408.

[21]Lv, L.S., Shao, X., Wang, L.Y., et al., 2010. Stilbene glucoside from Polygonum multiflorum Thunb.: a novel natural inhibitor of advanced glycation end product formation by trapping of methylglyoxal. J. Agric. Food Chem., 58(4):2239-2245.

[22]Malladi, A., Vashisth, T., Johnson, L.K., 2012. Ethephon and methyl jasmonate affect fruit detachment in rabbiteye and southern highbush blueberry. Hortscience, 47(12):1745-1749.

[23]Matsuoka, D., Yasufuku, T., Furuya, T., et al., 2015. An abscisic acid inducible Arabidopsis MAPKKK, MAPKKK18 regulates leaf senescence via its kinase activity. Plant Mol. Biol., 87(6):565-575.

[24]Miret, J.A., Cela, J., Bezerra, L.A., et al., 2014. Application of a rapid and sensitive method for hormonal and vitamin E profiling reveals crucial regulatory mechanisms in flower senescence and fruit ripening. J. Plant Growth Regul., 33(1):34-43.

[25]Misra, R.C., Maiti, P., Chanotiya, C.S., et al., 2014. Methyl jasmonate-elicited transcriptional responses and pentacyclic triterpene biosynthesis in sweet basil. Plant Physiol., 164(2):1028-1044.

[26]Moriya, Y., Itoh, M., Okuda, S., et al., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res., 35 (Suppl. 2):W182-W185.

[27]Mortazavi, A., Williams, B.A., Mccue, K., et al., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5(7):621-628.

[28]Mukkun, L., Singh, Z., 2009. Methyl jasmonate plays a role in fruit ripening of ‘Pajaro’ strawberry through stimulation of ethylene biosynthesis. Sci. Hortic., 123(1):5-10.

[29]Myhre, S., Tveit, H., Mollestad, T., et al., 2006. Additional gene ontology structure for improved biological reasoning. Bioinformatics, 22(16):2020-2027.

[30]Nopo-Olazabal, C., Condori, J., Nopo-Olazabal, L., et al., 2014. Differential induction of antioxidant stilbenoids in hairy roots of Vitis rotundifolia treated with methyl jasmonate and hydrogen peroxide. Plant Physiol. Biochem., 74:50-69.

[31]Vandesompele, J., de Preter, K., Pattyn, F., et al., 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol., 3(7):research0034.1-0034.11.

[32]Vannozzi, A., Dry, I.B., Fasoli, M., et al., 2012. Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses. BMC Plant Biol., 12(1):130.

[33]Repčák, M., Suvak, M., 2013. Methyl jasmonate and Echinothrips americanus regulate coumarin accumulation in leaves of Matricaria chamomilla. Biochem. Syst. Ecol., 47:38-41.

[34]Rice, P., Longden, I., Bleasby, A., 2000. EMBOSS: the European molecular biology open software suite. Trends Genet., 16(6):276-277.

[35]Rivera-Dominguez, M., Astorga-Cienfuegos, K.R., Tiznado-Hernandez, M.E., et al., 2012. Induction of the expression of defence genes in Carica papaya fruit by methyl jasmonate and low temperature treatments. Electron J. Biotech., 15(5):6.

[36]Sabater-Jara, A.B., Almagro, L., Pedreno, M.A., 2014. Induction of extracellular defense-related proteins in suspension cultured-cells of Daucus carota elicited with cyclodextrins and methyl jasmonate. Plant Physiol. Biochem., 77:133-139.

[37]Sayyari, M., Babalar, M., Kalantari, S., et al., 2011. Vapour treatments with methyl salicylate or methyl jasmonate alleviated chilling injury and enhanced antioxidant potential during postharvest storage of pomegranates. Food Chem., 124(3):964-970.

[38]Sivanandhan, G., Arun, M., Mayavan, S., et al., 2012. Optimization of elicitation conditions with methyl jasmonate and salicylic acid to improve the productivity of withanolides in the adventitious root culture of Withania somnifera (L.) Dunal. Appl. Biochem. Biotech., 168(3):681-696.

[39]Sun, G.L., Yang, Y.F., Xie, F.L., et al., 2013. Deep sequencing reveals transcriptome re-programming of taxus X media cells to the elicitation with methyl jasmonate. PLoS ONE, 8(4):e62865.

[40]Sun, J.W., Zhang, H., Wang, F.Y., et al., 2013. Effects of methyl jasmonate on accumulation and release of main tropane alkaloids in liquid cultures of Datura stramonium hairy root. China J. Chin. Mater. Med., 38(11):1712-1718 (in Chinese).

[41]Takahashi, I., Hara, M., 2014. Enhancement of starch accumulation in plants by exogenously applied methyl jasmonate. Plant Biotech. Rep., 8(2):143-149.

[42]Tatusov, R.L., Galperin, M.Y., Natale, D.A., et al., 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28(1):33-36.

[43]Thimm, O., Blasing, O., Gibon, Y., et al., 2004. Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37(6):914-939.

[44]Yan, C.Y., Zhang, Z., Yu, R.M., et al., 2007. Studies on biotransformation of arbutin by 4-hydroxy phenol in hairy root of Polygonum multiflorum. China J. Chin. Mater. Med., 32(3):192-195 (in Chinese).

[45]Ye, J., Fang, L., Zheng, H.K., et al., 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res., 34(Suppl. 2):W293-W297.

[46]Zhang, L.J., Wang, G., Zhang, F.M., et al., 2013. Soaking seeds in methyl jasmonate or benzothiadiazole induces resistance to an insect pest and stem decay in Brassica campestris L. ssp. chinensis. J. Hortic. Sci. Biotech., 88(6):715-720.

[47]Zheljazkov, V.D., Astatkie, T., Jeliazkova, E., 2013. Effect of foliar application of methyl jasmonate and extracts of juniper and sagebrush on essential oil yield and composition of ‘Native’ spearmint. HortScience, 48(4):462-465.

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 - 2023 Journal of Zhejiang University-SCIENCE