AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
PDF (4.7 MB)
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Review | Open Access

Multilayered regulation of secondary metabolism in medicinal plants

Yan Zhao1,2,Guanze Liu1,Feng Yang3,Yanli Liang1,2,Qingqing Gao1,2Chunfan Xiang1,2Xia Li1,2Run Yang1,2Guanghui Zhang1,2Huifeng Jiang4( )Lei Yu5( )Shengchao Yang1( )
Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201 Kunming, China
College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming 650201, China
Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, China
Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming 650214, China

Yan Zhao, Guanze Liu, Feng Yang and Yanli Liang contributed equally to this work.

Show Author Information

Abstract

Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.

Electronic Supplementary Material

Download File(s)
mh-3-2-11_ESM1.docx (50.5 KB)
mh-3-2-11_ESM2.docx (56.2 KB)
mh-3-2-11_ESM3.docx (43 KB)
mh-3-2-11_ESM4.docx (38.2 KB)
mh-3-2-11_ESM5.docx (44.8 KB)

References

 

Abbas F, Ke Y, Yu R, Yue Y, Amanullah S, Jahangir MM, Fan Y. Volatile terpenoids: multiple functions, biosynthesis, modulation and manipulation by genetic engineering. Planta. 2017;246:803–16. https://doi.org/10.1007/s00425-017-2749-x.

 

Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4:101. https://doi.org/10.7554/eLife.05005.

 

Ahmad A, Zhang Y, Cao XF. Decoding the epigenetic language of plant development. Mol Plant. 2010;3(4):719–28. https://doi.org/10.1093/mp/ssq026.

 

Ajikumar PK, Xiao WH, Tyo KE, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science. 2010;330(6000):70–4. https://doi.org/10.1126/science.1191652.

 

Akagi T, Katayama-Ikegami A, Kobayashi S, Sato A, Kono A, Yonemori K. Seasonal abscisic acid signal and a basic leucine zipper transcription factor, DkbZIP5, regulate proanthocyanidin biosynthesis in persimmon fruit. Plant Physiol. 2012;158(2):1089–102. https://doi.org/10.1104/pp.111.191205.

 

Ali Z, Syeda K, Ihsan F, Rabia J, Muhammad K, Asif R. Functions of plant’s bZIP transcription factors. Pak J Agric Sci. 2016;53:303-314. https://doi.org/10.21162/PAKJAS/16.2043.

 

Alonso R, Oñate-Sánchez L, Weltmeier F, Ehlert A, Diaz I, Dietrich K. A pivotal role of the basic leucine zipper transcription factor bZIP53 in the regulation of Arabidopsis seed maturation gene expression based on heterodimerization and protein complex formation. Plant Cell. 2009;21(6):1747–61. https://doi.org/10.1105/tpc.108.062968.

 

Ambawat S, Sharma P, Yadav NR, Yadav RC. MYB transcription factor genes as regulators for plant responses: an overview. Physiol Mol Biol Plants. 2013;19(3):307–21. https://doi.org/10.1007/s12298-013-0179-1.

 

Ayachit G, Shaikh I, Sharma P, Jani B, Shukla L, Sharma P, Bhairappanavar S, Joshi C, Das J. De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway. Sci Rep. 2019;9:14876. https://doi.org/10.1038/s41598-019-51355-x.

 

Bakshi M, Oelmüller R. WRKY transcription factors. Plant Signal Behav. 2014;9(2):e27700. https://doi.org/10.4161/psb.27700.

 

Bartel DP. MicroRNAs: Target Recognition and Regulatory Functions. Cell. 2009;136:215–33. https://doi.org/10.1016/j.cell.2009.01.002.

 

Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L. TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J. 2004;39(3):366–80. https://doi.org/10.1111/j.1365-313X.2004.02138.x.

 

Bird A. Perceptions of epigenetics. Nature. 2007;447:396–8. https://doi.org/10.1038/nature05913.

 

Biswas S, Hazra S, Chattopadhyay S. Identification of conserved miRNAs and their putative target genes in Podophyllum hexandrum (Himalayan Mayapple). Plant Gene. 2016;6:82–9. https://doi.org/10.1016/j.plgene.2016.04.002.

 

Boke H, Ozhuner E, Turktas M, Parmaksiz I, Ozcan S, Unver T. Regulation of the alkaloid biosynthesis by miRNA in opium poppy. Plant Biotechnol J. 2015;13(3):409–20. https://doi.org/10.1111/pbi.12346.

 

Borevitz JO, Xia Y, Blount J, Dixon RA, Lamb C. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell. 2000;12(12):2383–94. https://doi.org/10.1105/tpc.12.12.2383.

 

Bulut B, Aydinli Z, Türktaş-Erken M. MSAP analysis reveals diverse epigenetic statuses in opium poppy varieties with different benzyisoquinoline alkaloid content. Turkish J Biol. 2020;44(2):103–9. https://doi.org/10.3906/biy-1911-69.

 

Cao WZ, Wang Y, Shi M, Hao XL, Zhao WW, Wang Y, Ren J, Kai GY. Transcription factor SmWRKY1 positively promotes the biosynthesis of tanshinones in Salvia miltiorrhiza. Front Plant Sci. 2018;9:554. https://doi.org/10.3389/fpls.2018.00554.

 

Cao YP, Li K, Li YL, Zhao XP, Wang LH. MYB transcription factors as regulators of secondary metabolism in plants. Biology. 2020;9(3):61. https://doi.org/10.3390/biology9030061.

 

Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10(5):295–304. https://doi.org/10.1038/nrg2540.

 

Chang CH, Liu ZW, Wang YY, Tang ZH, Yu F. A bZIP transcription factor, CaLMF, mediated light-regulated camptothecin biosynthesis in Camptotheca acuminata. Tree Physiol. 2019;39(3):372–80. https://doi.org/10.1093/treephys/tpy106.

 

Chatel G, Montiel G, Pré M, Memelink J, Thiersault M, Saint-Pierre B, Doireau P, Gantet P. CrMYC1, a Catharanthus roseus elicitor- and jasmonate-responsive bHLH transcription factor that binds the G-box element of the strictosidine synthase gene promoter. J Exp Bot. 2003;54(392):2587–8. https://doi.org/10.1093/jxb/erg275.

 

Chen J, Zhou YH, Zhang Q, Liu Q, Li L, Sun CY, Wang KY, Wang YF, Zhao MZ, Li HJ, Han YL, Chen P, Li RQ, Lei J, Zhang MP, Wang Y. Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer. PloS One. 2020;15(3):e0226055. https://doi.org/10.1371/journal.pone.0226055.

 

Chen MH, Yan TX, Shen Q, Lu X, Pan QF, Huang YR, Tang YL, Fu XQ, Liu M, Jiang WM, Lv ZY, Shi P, Ma YN, Hao XL, Zhang LD, Li L, Tang KX. GLANDULAR TRICHOME-SPECIFIC WRKY 1 promotes artemisinin biosynthesis in Artemisia annua. New Phytol. 2017;214(1):304–16. https://doi.org/10.1111/nph.14373.

 

Chen Y, Wang YT, Guo J, Yang J, Zhang XD, Wang ZX, Cheng Y, Du ZW, Qi ZC, Huang YB, Dennis M, Wei YK, Yang DF, Huang LQ, Liang ZS. Integrated transcriptomics and proteomics to reveal regulation mechanism and evolution of SmWRKY61 on tanshinone biosynthesis in Salvia miltiorrhiza and Salvia castanea. Front Plant Sci. 2022;12:820582. https://doi.org/10.3389/fpls.2021.820582.

 

Cheynier V, Comte G, Davies KM, Lattanzio V, Martens S. Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology. Plant Physiol Biochem. 2013;72:1–20. https://doi.org/10.1016/j.plaphy.2013.05.009.

 

Chu Y, Xiao SM, Su H, Liao BS, Zhang JJ, Xu J, Chen SL. Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng. Acta Pharm Sin B. 2018;8(4):666–77. https://doi.org/10.1016/j.apsb.2018.04.004.

 

Chuang YC, Hung YC, Tsai WC, Chen WH, Chen HH. PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids. J Exp Bot. 2018;69(18):4363–77. https://doi.org/10.1093/jxb/ery246.

 

Deng B, Huang ZJ, Ge F, Liu DQ, Lu RJ, Chen CY. An AP2/ERF family transcription factor PnERF1 raised the biosynthesis of saponins in Panax notoginseng. J Plant Growth Regul. 2017;36:691–701. https://doi.org/10.1007/s00344-017-9672-z.

 

Deng CP, Hao XL, Shi M, Fu R, Wang Y, Zhang Y, Zhou W, Feng Y, Makunga NP, Kai GY. Tanshinone production could be increased by the expression of SmWRKY2 in Salvia miltiorrhiza hairy roots. Plant Sci. 2019;284:1–8. https://doi.org/10.1016/j.plantsci.2019.03.007.

 

Deng CP, Shi M, Fu R, Zhang Y, Wang Q, Zhang Y, Wang Y, Ma XY, Kai GY. ABA-responsive transcription factor bZIP1 is involved in modulating biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. J Exp Bot. 2020;71(19):5948–62. https://doi.org/10.1093/jxb/eraa295.

 

Deng CP, Wang Y, Huang FF, Lu SJ, Zhao LM, Ma XY, Kai GY. SmMYB2 promotes salvianolic acid biosynthesis in the medicinal herb Salvia miltiorrhiza. J Integr Plant Biol. 2020;62(11):1688–702. https://doi.org/10.1111/jipb.12943.

 

Deng Y, Lu S. Biosynthesis and regulation of phenylpropanoids in plants. Crit Rev Plant Sci. 2017;36(4):257–90. https://doi.org/10.1080/07352689.2017.1402852.

 

Di P, Wang P, Yan M, Han P, Huang XY, Yin L, Yan Y, Xu YH, Wang YP. Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng. BMC Genom. 2021;22(1):834. https://doi.org/10.1186/s12864-021-08145-5.

 

Dröge-Laser W, Snoek BL, Snel B, Weiste C. The Arabidopsis bZIP transcription factor family-an update. Curr Opin Plant Biol. 2018;45:36–49. https://doi.org/10.1016/j.pbi.2018.05.001.

 

Dröge-Laser W, Weiste C. The C/S1 bZIP Network: A regulatory hub orchestrating plant energy homeostasis. Trends Plant Sci. 2018;23(5):422–33. https://doi.org/10.1016/j.tplants.2018.02.003.

 

Du TZ, Niu JF, Su J, Li SS, Guo XR, Li L, Cao XY, Kang JF. SmbHLH37 functions antagonistically with SmMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza. Front Plant Sci. 2018;9:1720. https://doi.org/10.3389/fpls.2018.01720.

 

Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010;15(10):573–81. https://doi.org/10.1016/j.tplants.2010.06.005.

 

Dudareva N, Negre F, Nagegowda DA, Orlova I. Plant volatiles: recent advances and future perspectives. Crit Rev Plant Sci. 2006;25:417–40. https://doi.org/10.1080/07352680600899973.

 

Dugé de Bernonville T, Maury S, Delaunay A, Daviaud C, Chaparro C, Tost J, O’Connor SE, Courdavault V. Developmental methylome of the medicinal plant Catharanthus roseus unravels the tissue-specific control of the monoterpene indole alkaloid pathway by DNA methylation. Int J Mol Sci. 2020;21(17):6028. https://doi.org/10.3390/ijms21176028.

 

Elomaa P, Mehto M, Kotilainen M, Helariutta Y, Nevalainen L, Teeri TH. A bHLH transcription factor mediates organ, region and flower type specific signals on dihydroflavonol-4-reductase (dfr) gene expression in the inflorescence of Gerbera hybrida (Asteraceae). Plant J. 1998;16(1):93–9. https://doi.org/10.1046/j.1365-313x.1998.00273.x.

 

Ernst HA, Olsen AN, Larsen S, Lo Leggio L. Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors. EMBO Rep. 2004;5(3):297–303. https://doi.org/10.1038/sj.embor.7400093.

 

Eulgem T, Rushton PJ, Robatzek S, Somssich IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000;5(5):199–206. https://doi.org/10.1016/S1360-1385(00)01600-9.

 

Fan D, Wang XQ, Tang XF, Ye X, Ren S, Wang DH, Luo KM. Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar. Plant J. 2018;96(6):1121–36. https://doi.org/10.1111/tpj.14092.

 

Fan RY, Li YJ, Li CF, Zhang YS. Differential microRNA analysis of glandular trichomes and young leaves in Xanthium strumarium L. reveals their putative roles in regulating terpenoid biosynthesis. PLoS One. 2015;10:e0139002. https://doi.org/10.1371/journal.pone.0139002.

 

Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol. 2020;40(6):750–76. https://doi.org/10.1080/07388551.2020.1768509.

 

Fricke J, Hillebrand A, Twyman RM, Prüfer D, Schulze Gronover C. Abscisic acid-dependent regulation of Small Rubber Particle Protein gene expression in Taraxacum brevicorniculatum is mediated by TbbZIP1. Plant Cell Physiol. 2013;54(4):448–64. https://doi.org/10.1093/pcp/pcs182.

 

Fu XQ, Peng BW, Hassani D, Xie LH, Liu H, Li YP, Chen TT, Liu P, Tang YL, Li L, Zhao JY, Sun XF, Tang KX. AaWRKY9 contributes to light- and jasmonate-mediated to regulate the biosynthesis of artemisinin in Artemisia annua. New Phytol. 2021;231(5):1858–74. https://doi.org/10.1111/nph.17453.

 

Galanie S, Thodey K, Trenchard IJ, Filsinger Interrante M, Smolke CD. Complete biosynthesis of opioids in yeast. Science. 2015;349(6252):1095–100. https://doi.org/10.1126/science.aac9373.

 

Gao QQ, Song WL, Li X, Xiang CF, Chen G, Xiang GS, Liu XY, Zhang GH, Li XN, Yang SC, Zhai CX, Zhao Y. Genome-wide identification of bHLH transcription factors: Discovery of a candidate regulator related to flavonoid biosynthesis in Erigeron breviscapus. Front Plant Sci. 2022;13:977649. https://doi.org/10.3389/fpls.2022.977649.

 

Gani U, Vishwakarma RA, Misra P. Membrane transporters: the key drivers of transport of secondary metabolites in plants. Plant Cell Rep. 2021;40:1–18. https://doi.org/10.1007/s00299-020-02599-9.

 

Gao Z, Li J, Luo M, Li H, Chen QJ, Wang L, Song SR, Zhao LP, Xu WP, Zhang CX, Wang SP, Ma C. Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1. Plant Physiol. 2019;180:966–85. https://doi.org/10.1104/pp.18.01331.

 

Gehring M, Bubb KL, Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science. 2009;324(5933):1447–51. https://doi.org/10.1126/science.1171609.

 

Ghasemzadeh A, Jaafar HZ. Effect of CO2 enrichment on synthesis of some primary and secondary metabolites in ginger (Zingiber officinale Roscoe). Int J Mol Sci. 2011;12(2):1101–14. https://doi.org/10.3390/ijms12021101.

 

Gong ZZ, Yamagishi E, Yamazaki M, Saito K. A constitutively expressed Myc-like gene involved in anthocyanin biosynthesis from Perilla frutescens: molecular characterization, heterologous expression in transgenic plants and transactivation in yeast cells. Plant Mol Biol. 1999;41(1):33–44. https://doi.org/10.1023/a:1006237529040.

 

Gonzalez A, Zhao M, Leavitt JM, Lloyd AM. Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J. 2008;53(5):814–27. https://doi.org/10.1111/j.1365-313X.2007.03373.x.

 

Goodrich J, Carpenter R, Coen ES. A common gene regulates pigmentation pattern in diverse plant species. Cell. 1992;68(5):955–64. https://doi.org/10.1016/0092-8674(92)90038-e.

 

Goossens J, Mertens J, Goossens A. Role and functioning of bHLH transcription factors in jasmonate signalling. J Exp Bot. 2017;68(6):1333–47. https://doi.org/10.1093/jxb/erw440.

 

Han J, Liu HT, Wang SC, Wang CR, Miao GP. A class I TGA transcription factor from Tripterygium wilfordii Hook.f. modulates the biosynthesis of secondary metabolites in both native and heterologous hosts. Plant Sci. 2020;290:110293. https://doi.org/10.1016/j.plantsci.2019.110293.

 

Han YL, Cai MH, Zhang SQ, Chai JW, Sun MZ, Wang YW, Xie QY, Chen YH, Wang HZ, Chen T. Genome-wide identification of AP2/ERF transcription factor family and functional analysis of DcAP2/ERF#96 associated with abiotic stress in Dendrobium catenatum. Int J Mol Sci. 2022;23(21):13603. https://doi.org/10.3390/ijms232113603.

 

Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. Chinese Herb Med. 2018;10(3):239–48. https://doi.org/10.1016/j.chmed.2018.02.003.

 

Hao MZ, Zhou YH, Zhou JH, Zhang M, Yan KJ, Jiang S, Wang WS, Peng XP, Zhou S. Cold-induced ginsenosides accumulation is associated with the alteration in DNA methylation and relative gene expression in perennial American ginseng (Panax quinquefolius L.) along with its plant growth and development process. J Ginseng Res. 2020;44(5):747-755. https://doi.org/10.1016/j.jgr.2019.06.006.

 

Hao XL, Wang C, Zhou W, Ruan QY, Xie CH, Yang YK, Xiao CY, Cai Y, Wang JY, Wang Y, Zhang XB, Maoz I, Kai GY. OpNAC1 transcription factor regulates the biosynthesis of the anticancer drug camptothecin by targeting loganic acid O-methyltransferase in Ophiorrhiza pumila. J Integr Plant Biol. 2023;65(1):133–49. https://doi.org/10.1111/jipb.13377.

 

Hao XL, Zhong YJ, Nï Tzmann HW, Fu XQ, Yan TX, Shen Q, Chen MH, Ma YN, Zhao JY, LiL, Tang KX. Light-induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annua. Plant Cell Physiol. 2019;60(8):1747-1760. https://doi.org/10.1093/pcp/pcz084.

 

Hassan B. Medicinal plants (importance and uses). Pharmaceutica Anal Acta. 2013;03(10). https://doi.org/10.4172/2153-2435.1000e139.

 

He XJ, Chen T, Zhu JK. Regulation and function of DNA methylation in plants and animals. Cell Res. 2011;21:442–65. https://doi.org/10.1038/cr.2011.23.

 

Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC. The Basic Helix-Loop-Helix transcription factor family in plants: A genome-wide study of protein structure and functional diversity. Mol Biol Evol. 2003;20(5):735–47. https://doi.org/10.1093/molbev/msg088.

 

Heithoff DM, Sinsheimer RL, Low DA, Mahan MJ. An essential role for DNA adenine methylation in bacterial virulence. Science. 1999;284(5416):967–70. https://doi.org/10.1126/science.284.5416.967.

 

Hossain MA, Cho JI, Han M, Ahn CH, Jeon JS, An GH, Park PB. The ABRE-binding bZIP transcription factor OsABF2 is a positive regulator of abiotic stress and ABA signaling in rice. J Plant Physiol. 2010;167(17):1512–20. https://doi.org/10.1016/j.jplph.2010.05.008.

 

Huang D, Ming RH, Xu SQ, Yang SC, Li LB, Huang RS, Tan Y. Genome-wide identification of R2R3-MYB transcription factors: Discovery of a "Dual-Function" regulator of gypenoside and flavonol biosynthesis in Gynostemma pentaphyllum. Front Plant Sci. 2022;12:796248. https://doi.org/10.3389/fpls.2021.796248.

 

Huang HZ, Xing SH, Tang KX, Jiang WM. AaWRKY4 upregulates artemisinin content through boosting the expressions of key enzymes in artemisinin biosynthetic pathway. Plant Cell Tiss Organ Cult. 2021;146:97–105. https://doi.org/10.1007/s11240-021-02049-8.

 

Huang WJ, Khaldun AB, Chen JJ, Zhang CJ, Lv HY, Yuan L, Wang Y. A R2R3-MYB transcription factor regulates the flavonol biosynthetic pathway in a traditional Chinese medicinal plant, Epimedium sagittatum. Front Plant Sci. 2016;7:1089. https://doi.org/10.3389/fpls.2016.01089.

 

Huang WJ, Khaldun AB, Lv HY, Du LW, Zhang CJ, Wang Y. Isolation and functional characterization of a R2R3-MYB regulator of the anthocyanin biosynthetic pathway from Epimedium sagittatum. Plant Cell Rep. 2016;35(4):883–94. https://doi.org/10.1007/s00299-015-1929-z.

 

Huang WY, Lv HY, Wang Y. Functional characterization of a novel R2R3-MYB transcription factor modulating the flavonoid biosynthetic pathway from Epimedium sagittatum. Front Plant Sci. 2017;8:1274. https://doi.org/10.3389/fpls.2017.01274.

 

Huang WY, Sun W, Lv HY, Luo M, Zeng SH, Pattanaik S, Yuan L, Wang Y. A R2R3-MYB transcription factor from Epimedium sagittatum regulates the flavonoid biosynthetic pathway. PLoS One. 2013;8(8):e70778. https://doi.org/10.1371/journal.pone.0070778.

 

Ishiguro S, Nakamura K. Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5’ upstream regions of genes coding for sporamin and β-amylase from sweet potato. Mol Gen Genet. 1994;244(6):563–71. https://doi.org/10.1007/BF00282746.

 

Ito H, Gaubert H, Bucher E, Mirouze M, Vaillant I, Paszkowski J. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature. 2011;472:115–9. https://doi.org/10.1038/nature09861.

 

Jamwal K, Bhattacharya S, Puri S. Plant growth regulator mediated consequences of secondary metabolites in medicinal plants. J Appl Res Med Aroma. 2018;9:26–38. https://doi.org/10.1016/j.jarmap.2017.12.003.

 

Jan R, Asaf S, Numan M, Lubna, Kim KM. Plant secondary metabolite biosynthesis and transcriptional regulation in response to biotic and abiotic stress conditions. Agronomy. 2021;11(5):968. https://doi.org/10.3390/agronomy11050968.

 

Jarvis D, Ho YS, Lightfoot D, Schmöckel S, Li B, Borm TA, Ohyanagi H, Mineta K, Michell C, Saber N, Kharbatia N, Rupper R, Sharp A, Dally N, Boughton B, Woo Y, Gao G, Schijlen E, Guo XJ, Momin A, Negrão S, Al-Babili S, Gehring C, Roessner U, Tester M. The genome of Chenopodium quinoa. Nature. 2017;542:307–12. https://doi.org/10.1038/nature21370.

 

Ji AJ, Luo HM, Xu ZC, Zhang X, Zhu YJ, Liao BS, Yao H, Song JY, Chen SL. Genome-wide identification of the AP2/ERF gene family involved in active constituent biosynthesis in Salvia miltiorrhiza. Plant Genome. 2016;9(2). https://doi.org/10.3835/plantgenome2015.08.0077.

 

Ji YP, Xiao JW, Shen YL, Ma DM, Li ZQ, Pu GB, Li X, Huang LL, Liu BY, Ye HC, Wang H. Cloning and characterization of AabHLH1, a bHLH transcription factor that positively regulates artemisinin biosynthesis in Artemisia annua. Plant cell physiol. 2014;55(9):1592–604. https://doi.org/10.1093/pcp/pcu090.

 

Jia YY, Bai ZQ, Pei TL, Ding K, Liang ZS, Gong YH. The Protein kinase SmSnRK2.6 positively regulates phenolic acid biosynthesis in Salvia miltiorrhiza by interacting with SmAREB1. Front Plant Sci. 2017;8:1384. https://doi.org/10.3389/fpls.2017.01384.

 

Jiang JJ, Ma SH, Ye NH, Jiang M, Cao JS, Zhang JH. WRKY transcription factors in plant responses to stresses. J Integr Plant Biol. 2017;59(2):86–101. https://doi.org/10.1111/jipb.12513.

 

Jiang M, Chen H, Du Q, Wang L, Liu X, Liu C. Genome-wide identification of circular RNAs potentially involved in the biosynthesis of secondary metabolites in Salvia miltiorrhiza. Front in Genet. 2021;12:645115. https://doi.org/10.3389/fgene.2021.645115.

 

Kavas M, Baloğlu MC, Atabay ES, Ziplar UT, Daşgan HY, Ünver T. Genome-wide characterization and expression analysis of common bean bHLH transcription factors in response to excess salt concentration. Mol Genet Genomics. 2016;291:129–43. https://doi.org/10.1007/s00438-015-1095-6.

 

Kim J, Kang SH, Park SG, Yang TJ, Lee Y, Kim OT, Chung O, Lee J, Choi JP, Kwon SJ, Lee K, Ahn BO, Lee DJ, Yoo SI, Shin IG, Um Y, Lee DY, Kim GS, Hong CP, Bhak J, Kim CK. Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant. Hortic Res. 2020;7:112. https://doi.org/10.1038/s41438-020-0329-x.

 

Kiselev KV, Tyunin AP, Manyakhin AY, Zhuravlev YN. Resveratrol content and expression patterns of stilbene synthase genes in Vitis amurensis cells treated with 5-azacytidine. Plant Cell Tiss Organ Cult. 2011;105:65–72. https://doi.org/10.1007/s11240-010-9842-1.

 

Kooke R, Morgado L, Becker F, Eekelen H, Hazarika R, Zheng QF, de Vos R, Johannes F, Keurentjes J. Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. Genome Res. 2019;29(1):96–106. https://doi.org/10.1101/gr.232371.117.

 

Kumar P, Padhan JK, Kumar A, Chauhan RS. Transcriptomes of Podophyllum hexandrum unravel candidate miRNAs and their association with the biosynthesis of secondary metabolites. J Plant Biochem and Biotechnol. 2018;27:46–54. https://doi.org/10.1007/s13562-017-0414-x.

 

Kumar S, Singh AK, Mohapatra T. Epigenetics: history, present status and future perspective. Indian J Genet Plant Breed. 2017;77:445–63.

 

Lenka SK, Nims NE, Vongpaseuth K, Boshar RA, Roberts SC, Walker EL. Jasmonate-responsive expression of paclitaxel biosynthesis genes in Taxus cuspidata cultured cells is negatively regulated by the bHLH transcription factors TcJAMYC1, TcJAMYC2, and TcJAMYC4. Front Plant Sci. 2015;6:115. https://doi.org/10.3389/fpls.2015.00115.

 

Leung J, Gaudin V. Who Rules the Cell? An Epi-Tale of histone, DNA, RNA, and the metabolic deep state. Front Plant Sci. 2020;11:181. https://doi.org/10.3389/fpls.2020.00181.

 

Li CY, Leopold AL, Sander GW, Shanks JV, Zhao L, Gibson SI. CrBPF1 overexpression alters transcript levels of terpenoid indole alkaloid biosynthetic and regulatory genes. Front Plant Sci. 2015;6:818. https://doi.org/10.3389/fpls.2015.00818.

 

Li DQ, Shao FJ, Lu SF. Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza. Planta. 2015;241(5):1131–43. https://doi.org/10.1007/s00425-015-2246-z.

 

Li J, Li CL, Lu SF. Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia Miltiorrhiza. Peer J. 2018;6:e4461. https://doi.org/10.7717/peerj.4461.

 

Li M, Sun L, Gu H, Cheng DW, Guo XZ, Chen R, Wu ZY, Jiang JF, Fan XC, Chen JY. Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii). Sci Rep. 2021;11(1):6863. https://doi.org/10.1038/s41598-021-85754-w.

 

Li MR, Shi FX, Li YL, Jiang P, Jiao L, Liu B, Li LF. Genome-wide variation patterns uncover the origin and selection in cultivated ginseng (Panax ginseng Meyer). Genome Biol Evol. 2017;9(9):2159–69. https://doi.org/10.1093/gbe/evx160.

 

Li MY, Liu JX, Hao JN, Feng K, Duan AQ, Yang QQ, Xu ZS, Xiong AS. Genomic identification of AP2/ERF transcription factors and functional characterization of two cold resistance-related AP2/ERF genes in celery (Apium graveolens L.). Planta. 2019a;250(4):1265-1280. https://doi.org/10.1007/s00425-019-03222-2.

 

Li WF, Ning GX, Mao J, et al. Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin. Planta. 2019b;250:1833–47. https://doi.org/10.1007/s00425-019-03266-4.

 

Li XX, Duan XP, Jiang HX, Sun YJ, Tang YP, Yuan Z, Guo JK, Liang WQ, Chen L, Yin JY, Ma H, Wang J, Zhang DB. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 2006;141(4):1167–84. https://doi.org/10.1104/pp.106.080580.

 

Li Y, Liu Y, Qi F, Deng C, Lu C, Huang H, Dai S. Establishment of virus-induced gene silencing system and functional analysis of ScbHLH17 in Senecio cruentus. Plant Physiol Biochem. 2020;147:272–9. https://doi.org/10.1016/j.plaphy.2019.12.024.

 

Li YL, Chen XL, Wang JQ, Zou GP, Wang L, Li XS. Two responses to MeJA induction of R2R3-MYB transcription factors regulate flavonoid accumulation in Glycyrrhiza uralensis Fisch. PLoS One. 2020;15(7):e0236565. https://doi.org/10.1371/journal.pone.0236565.

 

Licausi F, Ohme-Takagi M, Perata P. APETALA2/ethylene responsive factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs. New Phytol. 2013;199:639–49. https://doi.org/10.1111/nph.12291.

 

Liu CC, Chi C, Jin LJ, Zhu J, Yu JQ, Zhou YH. The bZip transcription factor HY5 mediates CRYɑ-induced anthocyanin biosynthesis in tomato. Plant Cell Environ. 2018;41(8):1762–75. https://doi.org/10.1111/pce.13171.

 

Liu DQ, Zhao Q, Cui XM, Chen R, Li X, Qiu BL, Ge F. A transcriptome analysis uncovers Panax notoginseng resistance to Fusarium solani induced by methyl jasmonate. Genes Genomics. 2019;41(12):1383–96. https://doi.org/10.1007/s13258-019-00865-z.

 

Liu J, Osbourn A, Ma P. MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Mol Plant. 2015;8(5):689–708. https://doi.org/10.1016/j.molp.2015.03.012.

 

Liu JQ, Gao FY. Ren JS, Lu XJ, Ren GJ, Wang R. A novel AP2/ERF transcription factor CR1 regulates the accumulation of vindoline and serpentine in Catharanthus roseus. Front Plant Sci. 2017;8:2082. https://doi.org/10.3389/fpls.2017.02082.

 

Liu L, Yang DF, Xing BC, Zhang CL, Lang ZS. SmMYB98b positive regulation to tanshinones in Salvia miltiorrhiza Bunge hairy roots. Plant Cell Tiss Organ Cult. 2020;140:459–67. https://doi.org/10.1007/s11240-019-01716-1.

 

Liu T, Luo T, Guo XQ, Zhou X, Zhou DH, Gui L, Zhang Y, Zhang R, Luo ZY. PgMYB2, a MeJA-responsive transcription factor, positively regulates the dammarenediol synthase gene expression in Panax Ginseng. Int J Mol Sci. 2019;20(9):2219. https://doi.org/10.3390/ijms20092219.

 

Liu S, Wang Y, Shi M, et al. SmbHLH60 and SmMYC2 antagonistically regulate phenolic acids and anthocyanins biosynthesis in Salvia miltiorrhiza. J Adv Res. 2022;42:205–19. https://doi.org/10.1016/j.jare.2022.02.005.

 

Liu WY, Chiou SJ, Ko CY, Lin TY. Functional characterization of three ethylene response factor genes from Bupleurum kaoi indicates that BkERFs mediate resistance to Botrytis cinerea. J Plant Physiol. 2011;168(4):375–81. https://doi.org/10.1016/j.jplph.2010.07.006.

 

Liu X, Yang S, Yu CW, Chen CY, Wu K. Chapter Six - Histone acetylation and plant development. The Enzymes. 2016;40:173–99. https://doi.org/10.1016/bs.enz.2016.08.001.

 

Liu XC, Yang SG, Zhao ML, Luo M, Yu CW, Chen CY, Ready Tai, Wu KQ. Transcriptional repression by histone deacetylases in plants. Mol Plant. 2014;7(5):764-772. https://doi.org/10.1093/mp/ssu033.

 

Liu YY, Zhu PP, Cai S, Haughn G, Page JE. Three novel transcription factors involved in cannabinoid biosynthesis in Cannabis sativa L. Plant Mol Biol. 2021;106(1–2):49–65. https://doi.org/10.1007/s11103-021-01129-9.

 

Luo X, Reiter MA, d’Espaux L, Wong J, Denby CM, Lechner A, Zhang Y, Grzybowski AT, Harth S, Lin W, Lee H. Complete biosynthesis of cannabinoids and their unnatural analogues in yeast. Nature. 2019;567(7746):123–6. https://doi.org/10.1038/s41586-019-0978-9.

 

Lv ZY, Guo ZY, Zhang LD, Zhang FY, Jiang WM, Shen Q, Fu XQ, Yan TX, Shi P, Hao XL, Ma YA, Chen MH, Li L, Zhang L, Chen WS, Tang KX. Interaction of bZIP transcription factor TGA6 with salicylic acid signaling modulates artemisinin biosynthesis in Artemisia annua. J Exp Bot. 2019;70(15):3969–79. https://doi.org/10.1093/jxb/erz166.

 

Lv ZY, Wang S, Zhang FY, Chen LX, Hao XL, Pan QF, Fu XQ, Li L, Sun XF, Tang KX. Overexpression of a novel NAC domain-containing transcription factor gene (AaNAC1) enhances the content of artemisinin and increases tolerance to drought and Botrytis cinerea in Artemisia annua. Plant Cell Physiol. 2016;57(9):1961–71. https://doi.org/10.1093/pcp/pcw118.

 

Lv Z, Li J, Qiu S, Qi F, Su H, Bu Q, Jiang R, Tang K, Zhang L, Chen W. The transcription factors TLR1 and TLR2 negatively regulate trichome density and artemisinin levels in Artemisia annua. J Integr Plant Biol. 2022;64:1212–28. https://doi.org/10.1111/jipb.13258.

 

Ma DM, Pu GB, Lei CY, Ma LQ, Wang HH, Guo YW, Chen JL, Du ZG, Wang H, Li GF, Ye HC, Liu BY. Isolation and characterization of AaWRKY1, an Artemisia annua transcription factor that regulates the amorpha-4,11-diene synthase gene, a key gene of artemisinin biosynthesis. Plant Cell Physiol. 2009;50(12):2146–61. https://doi.org/10.1093/pcp/pcp149.

 

Ma RF, Xiao Y, Lv ZY, Tan HX, Chen RB, Li Q, Chen JF, Wang Y, Yin J, Zhang L, Chen WS. AP2/ERF transcription factor, Ii049, positively regulates lignan biosynthesis in Isatis indigotica through activating salicylic acid signaling and lignan/lignin pathway genes. Front Plant Sci. 2017;8:1361. https://doi.org/10.3389/fpls.2017.01361.

 

Ma Y, Li D, Zhong Y, Wang X, Li L, Osbourn A, Lucas WJ, Huang SW, Shang Y. Vacuolar MATE/DTX protein-mediated cucurbitacin C transport is co-regulated with bitterness biosynthesis in cucumber. New Phytol. 2023;238(3):995–1003. https://doi.org/10.1111/nph.18786.

 

Mao K, Dong QL, Li C, Liu CH, Ma FW. Genome Wide identification and characterization of Apple bHLH transcription factors and expression analysis in response to drought and salt stress. Front Plant Sci. 2017;8:480. https://doi.org/10.3389/fpls.2017.00480.

 

Martienssen RA, Colot V. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science. 2001;293(5532):1070–4. https://doi.org/10.1126/science.293.5532.1070.

 

Martin C, Paz-Ares J. MYB transcription factors in plants. Trends Genet. 1997;13(2):67–73. https://doi.org/10.1016/S0168-9525(96)10049-4.

 

Mehrtens F, Kranz H, Bednarek P, Weisshaar B. The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol. 2005;138(2):1083–96. https://doi.org/10.1104/pp.104.058032.

 

Menke FL, Champion A, Kijne JW, Memelink J. A novel jasmonate- and elicitor-responsive element in the periwinkle secondary metabolite biosynthetic gene Str interacts with a jasmonate- and elicitor-inducible AP2-domain transcription factor, ORCA2. EMBO J. 1999;18(16):4455–63. https://doi.org/10.1093/emboj/18.16.4455.

 

Mertens J, Pollier J, Vanden Bossche R, Lopez-Vidriero I, Franco-Zorrilla JM, Goossens A. The bHLH transcription factors TSAR1 and TSAR2 regulate triterpene ssaponin biosynthesis in Medicago truncatula. Plant Physiol. 2016;170(1):194–210. https://doi.org/10.1104/pp.15.01645.

 

Meyer P. Epigenetics - A historical perspective. Adv Bot Res. 2018;88:1–19. https://doi.org/10.1016/bs.abr.2018.08.003.

 

McElroy C, Jennewein S, Schwab W, Lange BM, Wüst M. Taxol® biosynthesis and production: from forests to fermenters. Biotechnology of natural products. 2018;145-185. https://doi.org/10.1007/978-3-319-67903-7_7.

 

Morita Y, Saito R, Ban Y, Tanikawa N, Kuchitsu K, Ando T, Yoshikawa M, Habu Y, Ozeki Y, Nakayama M. Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida. Plant J. 2012;70(5):739–49. https://doi.org/10.1111/j.1365-313X.2012.04908.x.

 

Morreel K, Saeys Y, Dima O, Lu F, Van de Peer Y, Vanholme R, Ralph J, Vanholme B, Boerjan W. Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks. Plant Cell. 2014;26:929–45. https://doi.org/10.1105/tpc.113.122242.

 

Nagegowda DA. Plant volatile terpenoid metabolism: biosynthetic genes, transcriptional regulation and subcellular compartmentation. FEBS Lett. 2010;584(14):2965–73. https://doi.org/10.1016/j.febslet.2010.05.045.

 

Najafabadi AS, Naghavi MR. Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes. Gene. 2018;645:41–7. https://doi.org/10.1016/j.gene.2017.12.035.

 

Nakatsuka T, Haruta KS, Pitaksutheepong C, Abe Y, Kakizaki Y, Yamamoto K, Shimada N, Yamamura S, Nishihara M. Identification and characterization of R2R3-MYB and bHLH transcription factors regulating anthocyanin biosynthesis in gentian flowers. Plant Cell Physiol. 2008;49(12):1818–29. https://doi.org/10.1093/pcp/pcn163.

 

Navarro M, Marque G, Ayax C, Keller G, Borges JP, Marque C, Teulières C. Complementary regulation of four Eucalyptus CBF genes under various cold conditions. J Exp Bot. 2009;60(9):2713–24. https://doi.org/10.1093/jxb/erp129.

 

Nijhawan A, Jain M, Tyagi AK, Khurana JP. Genomic survey and gene expression analysis of the basic Leucine Zipper transcription factor family in Rice. Plant Physiol. 2008;146(2):333–50. https://doi.org/10.1104/pp.107.112821.

 

Nims E, Vongpaseuth K, Roberts SC, Walker EL. TcJAMYC: a bHLH transcription factor that activates paclitaxel biosynthetic pathway genes in yew. J Biol Chem. 2015;290(33):20104. https://doi.org/10.1074/jbc.A109.026195.

 

Ning K, Li MZ, Wei GF, Zhou YX, Zhang GZ, Huai H, Wei FG, Chen ZJ, Wang Y, Dong LL, Chen SL. Genomic and transcriptomic analysis provide insights into Root Rot resistance in Panax notoginseng. Front Plant Sci. 2021;12:775019. https://doi.org/10.3389/fpls.2021.775019.

 

Ohno S, Hosokawa M, Hoshino A, Kitamura Y, Morita Y, Park KI, Nakashima A, Deguchi A, Tatsuzawa F, Doi M, Iida S, Yazawa S. A bHLH transcription factor, DvIVS, is involved in regulation of anthocyanin synthesis in dahlia (Dahlia variabilis). J Exp Bot. 2011;62(14):5105-5116. https://doi.org/10.1093/jxb/err216.

 

Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature. 2013;496(7446):528–32. https://doi.org/10.1038/nature12051.

 

Pagliarani C, Gambino G, Ferrandino A, Chitarra W, Vrhovsek U, Cantu D, Palmano S, Marzachì C, Schubert A. Molecular memory of Flavescence dorée phytoplasma in recovering grapevines. Hortic Res. 2020;7:126. https://doi.org/10.1038/s41438-020-00348-3.

 

Pan QF, Wang CY, Xiong ZW, Wang H, Fu XQ, Shen Q, Peng BW, Ma YN, Sun XF, Tang KX. CrERF5, an AP2/ERF transcription factor, positively regulates the biosynthesis of bisindole alkaloids and their precursors in Catharanthus roseus. Front Plant Sci. 2019;10:931. https://doi.org/10.3389/fpls.2019.00931.

 

Pani A, Mahapatra RK. Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. Genomics Data. 2013;1:2–6. https://doi.org/10.1016/j.gdata.2013.06.001.

 

Park KI, Ishikawa N, Morita Y, Choi JD, Hoshino A, Iida S. A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation. Plant J. 2007;641-654. https://doi.org/10.1111/j.1365-313X.2006.02988.x.

 

Park KI. A bHLH protein partially controls proanthocyanidin and phytomelanin pigmentation in the seed coats of morning glory Ipomoea tricolor. Hortic Environ Biotechnol. 2012;53:304–9. https://doi.org/10.1007/s13580-012-0006-6.

 

Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H. The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. EMBO J. 1987;6(12):3553–8. https://doi.org/10.1002/j.1460-2075.1987.tb02684.x.

 

Peng Z, Tian J, Luo RL, Kang YH, Lu YF, Hu YJ, Liu N, Zhang J, Cheng H, Niu SQ, Zhang J, Yao YC. MiR399d and epigenetic modification comodulate anthocyanin accumulation in Malus leaves suffering from phosphorus deficiency. Plant Cell Environ. 2020;43(5):1148–59. https://doi.org/10.1111/pce.13697.

 

Phukan UJ, Jeena GS, Tripathi V, Shukla RK. MaRAP2-4, a waterlogging-responsive ERF from Mentha, regulates bidirectional sugar transporter AtSWEET10 to modulate stress response in Arabidopsis. Plant Biotechnol J. 2018;16(1):221–33. https://doi.org/10.1111/pbi.12762.

 

Prakash P, Rajakani R, Gupta V. Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets. Comput Biol Chem. 2016;61:62–74. https://doi.org/10.1016/j.compbiolchem.2015.12.002.

 

Přibylová A, Čermák V, Tyč D, Fischer L. Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells. Epigenetics chromatin. 2019;12(1):54. https://doi.org/10.1186/s13072-019-0299-0.

 

Quattrocchio F, Wing JF, Leppen H, Mol J, Koes RE. Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes. Plant Cell. 1993;5(11):1497–512. https://doi.org/10.1105/tpc.5.11.1497.

 

Quattrocchio F, Wing JF, van der Woude K, Mol JN, Koes R. Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J. 1998;13(4):475–88. https://doi.org/10.1046/j.1365-313x.1998.00046.x.

 

Ribeiro B, Erffelinck ML, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M, Goossens A. Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. Front Plant Sci. 2022;13:903793. https://doi.org/10.3389/fpls.2022.903793.

 

Ribeiro B, Lacchini E, Bicalho KU, Mertens J, Arendt P, Vanden Bossche R, Calegario G, Gryffroy L, Ceulemans E, Buitink J, Goossens A, Pollier J. A seed-specific regulator of triterpene saponin biosynthesis in Medicago truncatula. Plant Cell. 2020;32(6):2020–42. https://doi.org/10.1105/tpc.19.00609.

 

Rodriguez-Concepcion M, Boronat A. Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics. Plant Physiol. 2002;130(3):1079-1089. https://doi.org/10.1104/pp.007138.

 

Rohani ER, Chiba M, Kawaharada M, Asano T, Oshima Y, Mitsuda N, Ohme-Takagi M, Fukushima A, Rai A, Saito K, Yamazaki M. An MYB transcription factor regulating specialized metabolisms in Ophiorrhiza pumila. Plant Biotechnol. 2016;33(1):1–9. https://doi.org/10.5511/plantbiotechnology.15.1117a.

 

Rushton PJ, Somssich IE, Ringler P, Shen QJ. WRKY transcription factors. Trends Plant Sci. 2010;15(5):247–58. https://doi.org/10.1016/j.tplants.2010.02.006.

 

Saifi M, Nasrullah N, Ahmad MM, Ali A, Khan JA, Abdin MZ. In silico analysis and expression profiling of miRNAs targeting genes of steviol glycosides biosynthetic pathway and their relationship with steviol glycosides content in different tissues of Stevia rebaudiana. Plant Physiol Biochem. 2015;94:57–64. https://doi.org/10.1016/j.plaphy.2015.05.009.

 

Sanchez-Muñoz R, Moyano E, Khojasteh A, Bonfill M, Cusido RM, Palazon J. Genomic methylation in plant cell cultures: A barrier to the development of commercial long-term biofactories. Eng Life Sci. 2019;19(12):872–9. https://doi.org/10.1002/elsc.201900024.

 

Sanchita, Sharma A. Gene expression analysis in medicinal plants under abiotic stress conditions. Plant metabolites and regulation under environmental stress. 2018;407-414. https://doi.org/10.1016/B978-0-12-812689-9.00023-6.

 

Schluttenhofer C, Yuan L. Regulation of specialized metabolism by WRKY transcription factors. Plant Physiol. 2015;167(2):295–306. https://doi.org/10.1104/pp.114.251769.

 

Shang Y, Ma YS, Zhou Y, Zhang HM, Duan LX, Chen HM, Zeng JG, Zhou Q, Wang SH, Gu WJ, Liu M, Ren JW, Gu XF, Zhang SP, Wang Y, Yasukawa K, Bouwmeester HJ, Qi XQ, Zhang ZH, Lucas WJ, Huang SW. Biosynthesis, regulation, and domestication of bitterness in cucumber. Science. 2014;346(6213):1084–8. https://doi.org/10.1126/science.1259215.

 

Sharma A, Shahzad B, Rehman A, Bhardwaj R, Landi M, Zheng B. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules. 2019;24(13):2452. https://doi.org/10.3390/molecules24132452.

 

Shen EM, Singh SK, Ghosh JS, Patra B, Paul P, Yuan L, Pattanaik S. The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis. Sci Rep. 2017;7(1):43027. https://doi.org/10.1038/srep43027.

 

Shen Q, Huang HY, Zhao Y, Xie LH, He Q, Zhong YJ, Wang YT, Wang YL, Tang KX. The transcription factor Aabzip9 positively regulates the biosynthesis of artemisinin in Artemisia annua. Front Plant Sci. 2019;10:1294. https://doi.org/10.3389/fpls.2019.01294.

 

Shi J, Xiong YJ, Zhang H, Meng X, Zhang ZY, Zhang MM, Yu JS, Zhu YF, Xue T, Xu JP. Analysis of shading on DNA methylation by MSAP in Pinellia ternata. Zhongguo Zhong yao za zhi. 2020;45(6):1311-1315. https://doi.org/10.19540/j.cnki.cjcmm.20200105.105.

 

Shi M, Du ZY, Hua Q, Kai GY. CRISPR/Cas9-mediated targeted mutagenesis of bZIP2 in Salvia miltiorrhiza leads to promoted phenolic acid biosynthesis. Ind Crop Prod. 2021;167:113560. https://doi.org/10.1016/j.indcrop.2021.113560.

 

Shi M, Zhu RY, Zhang Y, Zhang SW, Liu TY, Li KL, Liu SC, Wang LR, Wang Y, Zhou W, Hua Q, Kai GY. A novel WRKY34-bZIP3 module regulates phenolic acid and tanshinone biosynthesis in Salvia miltiorrhiza. Metabolic engineering. 2022;73:182–91. https://doi.org/10.1016/j.ymben.2022.08.002.

 

Shitan N, Kato K, Shoji T. Alkaloid transporters in plants. Plant Biotechnol. 2014;31:453–63. https://doi.org/10.5511/plantbiotechnology.14.1002a.

 

Shu GP, Tang YL, Yuan MY, Wei N, Zhang FY, Yang CX, Lan XZ, Chen M, Tang KX, Xiang L, Liao ZH, Liao Z. Molecular insights into AabZIP1-mediated regulation on artemisinin biosynthesis and drought tolerance in Artemisia annua. Acta Pharm Sin B. 2022;12(3):1500–13. https://doi.org/10.1016/j.apsb.2021.09.026.

 

Shukla RK, Raha S, Tripathi V, Chattopadhyay D. Expression of CAP2, an APETALA2-family transcription factor from Chickpea, enhances growth and tolerance to dehydration and salt stress in transgenic tobacco. Plant Physiol. 2006;142(1):113–23. https://doi.org/10.1104/pp.106.081752.

 

Sibéril Y, Benhamron S, Memelink J, Gantet P. Catharanthus roseus G-box binding factors 1 and 2 act as repressors of strictosidine synthase gene expression in cell cultures. Plant Mol Biol. 2001;45(4):477–88. https://doi.org/10.1023/a:1010650906695.

 

Song XM, Huang ZN, Duan WK, Ren J, Liu TK, Li Y, Hou XL. Genome-wide analysis of the bHLH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics. 2014;289(1):77-91. https://doi.org/10.1007/s00438-013-0791-3.

 

Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J. 2007;50(4):660–77. https://doi.org/10.1111/j.1365-313X.2007.03078.x.

 

Stracke R, Jahns O, Keck M, Tohge T, Niehaus K, Fernie AR, Weisshaar B. Analysis of PRODUCTION OF FLAVONOL GLYCOSIDES-dependent flavonol glycoside accumulation in Arabidopsis thaliana plants reveals MYB11-, MYB12- and MYB111-independent flavonol glycoside accumulation. New Phytol. 2010;188(4):985–1000. https://doi.org/10.1111/j.1469-8137.2010.03421.x.

 

Stracke R, Werber M, Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001;4(5):447–56. https://doi.org/10.1016/S1369-5266(00)00199-0.

 

Strahl B, Allis C. The language of covalent histone modifications. Nature. 2000;403:41–5. https://doi.org/10.1038/47412.

 

Suttipanta N, Pattanaik S, Kulshrestha M, Patra B, Singh SK, Yuan L. The transcription factor CrWRKY1 positively regulates the terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiol. 2011;157(4):2081–93. https://doi.org/10.1104/pp.111.181834.

 

Talanian RV, McKnight CJ, Kim PS. Sequence-specific DNA binding by a short peptide dimer. Science. 1990;249(4970):769–71. https://doi.org/10.1126/science.2389142.

 

Tamura K, Yoshida K, Hiraoka Y, Sakaguchi D, Chikugo A, Mochida K, Kojoma M, Mitsuda N, Saito K, Muranaka T, Seki H. The Basic Helix-Loop-Helix transcription factor GubHLH3 positively regulates soyasaponin biosynthetic genes in Glycyrrhiza uralensis. Plant Cell Physiol. 2018;59(4):778–91. https://doi.org/10.1093/pcp/pcy075.

 

Tang MJ, Sun JW, Liu Y, Chen F, Shen SH. Isolation and functional characterization of the JcERF gene, a putative AP2/EREBP domain-containing transcription factor, in the woody oil plant Jatropha curcas. Plant Mol Biol. 2007;63(3):419–28. https://doi.org/10.1007/s11103-006-9098-7.

 

Tang N, Cao ZY, Yang C, Ran DS, Wu PY, Gao HM, He N, Liu GH, Chen, Z. A R2R3-MYB transcriptional activator LmMYB15 regulates chlorogenic acid biosynthesis and phenylpropanoid metabolism in Lonicera macranthoides. Plant Sci. 2021;308,110924. https://doi.org/10.1016/j.plantsci.2021.110924.

 

Tetali SD. Terpenes and isoprenoids: a wealth of compounds for global use. Planta. 2019;249:1–8. https://doi.org/10.1007/s00425-018-3056-x.

 

Thakur S, Vasudev PG. MYB transcription factors and their role in Medicinal plants. Mol Biol Rep. 2022;49(11):10995–1008. https://doi.org/10.1007/s11033-022-07825-z.

 

Tian Q, Han LM, Zhu XY, Zhang CJ, Li YY, Xue XS, Wang YY, Wang DH, Niu JF, Hua WP, Li B, Wang ZZ. SmMYB4 is a R2R3-MYB transcriptional repressor regulating the biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. Metabolites. 2022;12(10):968. https://doi.org/10.3390/metabo12100968.

 

Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis Basic/Helix-Loop-Helix transcription factor family. Plant Cell. 2003;15(8):1749–70. https://doi.org/10.1105/tpc.013839.

 

Tu MX, Fang JH, Zhao RK, Liu XY, Yin WC, Wang Y, Wang XH, Wang XP, Fang YL. CRISPR/Cas9-mediated mutagenesis of VvbZIP36 promotes anthocyanin accumulation in grapevine (Vitis vinifera). Hortic Res. 2022;9:022. https://doi.org/10.1093/hr/uhac022.

 

Tuteja JH, Zabala G, Varala K, Hudson M, Vodkin LO. Endogenous, Tissue-specific short interfering RNAs silence the chalcone synthase gene family in Glycine max seed coats. Plant Cell. 2009;21(10):3063–77. https://doi.org/10.1105/tpc.109.069856.

 

Van Moerkercke A, Steensma P, Schweizer F, Pollier J, Gariboldi I, Payne R, Vanden Bossche R, Miettinen K, Espoz J, Purnama PC, Kellner F, Seppänen-Laakso T, O’Connor SE, Rischer H, Memelink J, Goossens A. The bHLH transcription factor BIS1 controls the iridoid branch of the monoterpenoid indole alkaloid pathway in Catharanthus roseus. Proc Natl Acad Sci USA. 2015;112(26):8130–5. https://doi.org/10.1073/pnas.1504951112.

 

Vanyushin BF, Ashapkin VV. DNA methylation in higher plants: Past, present and future. Biochim Biophys Acta Gene Regul Mech. 2011;1809(8):360–8. https://doi.org/10.1016/j.bbagrm.2011.04.006.

 

Vashisht I, Mishra P, Pal T, Chanumolu S, Singh TR, Chauhan RS. Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb. Picrorhiza kurroa Planta. 2015;241:1255–68. https://doi.org/10.1007/s00425-015-2255-y.

 

Vazquez F, Legrand S, Windels D. The biosynthetic pathways and biological scopes of plant small RNAs. Trends Plant Sci. 2010;15(6):337–45. https://doi.org/10.1016/j.tplants.2010.04.001.

 

Verma P, Singh N, Khan SA, Mathur AK, Sharma A, Jamal F. TIAs pathway genes and associated miRNA identification in Vinca minor: supporting aspidosperma and eburnamine alkaloids linkage via transcriptomic analysis. Physiol Mol Biol Plants. 2020;26:1695–711. https://doi.org/10.1007/s12298-020-00842-x.

 

Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F. Methylome evolution in plants. Genome Biol. 2016;17:264. https://doi.org/10.1186/s13059-016-1127-5.

 

Wang C, Hao XL, Wang Y, Maoz I, Zhou W, Zhou ZG, Kai GY. Identification of WRKY transcription factors involved in regulating the biosynthesis of the anti-cancer drug camptothecin in Ophiorrhiza pumila. Hortic Res. 2022;9:uhac099. https://doi.org/10.1093/hr/uhac099.

 

Wang D, Jiang CY, Li RM, Wang YJ. VqbZIP1 isolated from Chinese wild Vitis quinquangularis is involved in the ABA signaling pathway and regulates stilbene synthesis. Plant Sci. 2019;287:110202. https://doi.org/10.1016/j.plantsci.2019.110202.

 

Wang J, Meng X, Dobrovolskaya OB, Orlov YL, Chen M. Non-coding RNAs and their roles in stress response in plants. Genomics Proteomics Bioinformatics. 2017;15:301–12. https://doi.org/10.1016/j.gpb.2017.01.007.

 

Wang M, Wu B, Chen C, Lu S. Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng. J Integr Plant Biol. 2015;57(3):256–70. https://doi.org/10.1111/jipb.12239.

 

Wang S, Zhang X, Li B, Zhao X, Shen Y, Yuan Z. Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum). BMC Plant Biol. 2022;22(1):170. https://doi.org/10.1186/s12870-022-03560-6.

 

Wang WT, Hu SY, Yang J, Zhang CJ, Zhang T, Wang DH, Cao XY, Wang ZZ. A novel R2R3-MYB transcription factor SbMYB12 positively regulates baicalin biosynthesis in Scutellaria baicalensis Georgi. Int J Mol Sci. 2022a;23(24). https://doi.org/10.3390/ijms232415452.

 

Wang XB, Tang Y, Huang HL, Wu DD, Chen XZ, Li JR, Zheng H, Zhan RT, Chen LK. Functional analysis of Pogostemon cablin farnesyl pyrophosphate synthase gene and its binding transcription factor PcWRKY44 in regulating biosynthesis of patchouli alcohol. Front Plant Sci. 2022;13:946629. https://doi.org/10.3389/fpls.2022.946629.

 

Wani SH, Anand S, Singh B, Bohra A, Joshi R. WRKY transcription factors and plant defense responses: latest discoveries and future prospects. Plant Cell Rep. 2021;40(7):1071–85. https://doi.org/10.1007/s00299-021-02691-8.

 

Wu B, Li Y, Yan H, Ma Y, Luo H, Yuan L, Chen S, Lu S. Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics. 2012;13:15. https://doi.org/10.1186/1471-2164-13-15.

 

Wu ZKY, Li L, Liu H, Yan X, Ma YA, Li YP, Chen TT, Wang C, Xie LH, Hao XL, Tang KX. AaMYB15, an R2R3-MYB TF in Artemisia annua, acts as a negative regulator of artemisinin biosynthesis. Plant Sci. 2021;308:110920. https://doi.org/10.1016/j.plantsci.2021.110920.

 

Xia PG, Hu WY, Zheng YJ, Wang Y, Yan KJ, Liang ZS. Structural and interactions analysis of a transcription factor PnMYB2 in Panax notoginseng. J Plant Physiol. 2022;275:153756. https://doi.org/10.1016/j.jplph.2022.153756.

 

Xiang LL, Liu XF, Li X, Yin XR, Grierson D, Li F, Chen KS. A novel bHLH transcription factor involved in regulating anthocyanin biosynthesis in Chrysanthemums (Chrysanthemum morifolium Ramat.). PLoS One. 2015;10(11):e0143892. https://doi.org/10.1371/journal.pone.0143892.

 

Xiao L, Ren JZ, Li Q, Yang B, Liu ZJ, Chen RB, Zhang L. Genome-wide analysis of AP2/ERF superfamily in Isatis indigotica. J Integr Med. 2023;21(1):77–88. https://doi.org/10.1016/j.joim.2022.09.003.

 

Xie DY, Sharma SB, Wright E, Wang ZY, Dixon RA. Metabolic engineering of proanthocyanidins through co-expression of anthocyanidin reductase and the PAP1 MYB transcription factor. Plant J. 2006;45(6):895–907. https://doi.org/10.1111/j.1365-313X.2006.02655.x.

 

Xie LH, Yan TX, Li L, Chen MH, Ma YA, Hao XL, Fu XQ, Shen Q, Huang YW, Qin W, Liu H, Chen TT, Hassani D, Kayani SL, Rose JKC, Tang KX. The WRKY transcription factor AaGSW2 promotes glandular trichome initiation in Artemisia annua. J Exp Bot. 2021;72(5):1691–701. https://doi.org/10.1093/jxb/eraa523.

 

Xie ZM, Yang CY, Liu SY, Li MJ, Gu L, Peng X, Zhang ZY. Identification of AP2/ERF transcription factors in Tetrastigma hemsleyanum revealed the specific roles of ERF46 under cold stress. Front Plant Sci. 2022;13:936602. https://doi.org/10.3389/fpls.2022.936602.

 

Xu F, Ning YJ, Zhang WW, Liao YL, Li LL, Cheng H, Cheng SY. An R2R3-MYB transcription factor as a negative regulator of the flavonoid biosynthesis pathway in Ginkgo biloba. Funct Integr Genomics. 2014;14(1):177–89. https://doi.org/10.1007/s10142-013-0352-1.

 

Xu J, Wu SR, Xu YH, Ge ZY, Sui C, Wei JH. Overexpression of BcbZIP134 negatively regulates the biosynthesis of saikosaponins. Plant Cell Tiss Organ Cult. 2019;137:297–308. https://doi.org/10.1007/s11240-019-01571-0.

 

Yamada Y, Kokabu Y, Chaki K, Yoshimoto T, Ohgaki M, Yoshida S, Kato N, Koyama T, Sato F. Isoquinoline alkaloid biosynthesis is regulated by a unique bHLH-type transcription factor in Coptis japonica. Plant Cell Physiol. 2011;52(7):1131–41. https://doi.org/10.1093/pcp/pcr062.

 

Yamada Y, Nishida S, Shitan N, Sato F. Genome-wide profiling of WRKY genes involved in benzylisoquinoline alkaloid biosynthesis in California Poppy (Eschscholzia californica). Front Plant Sci. 2021;12:699326. https://doi.org/10.3389/fpls.2021.699326.

 

Yang CQ, Fang X, Wu XM, Mao YB, Wang LJ, Chen XY. Transcriptional regulation of plant secondary metabolism. J Integr Plant biol. 2012;54(10):703–12. https://doi.org/10.1111/j.1744-7909.2012.01161.x.

 

Yang DF, Huang ZC, Jin WB, Xia PG, Jia QJ, Yang ZQ, Hou ZN, Zhang HH, Ji W, Han RL. DNA methylation: A new regulator of phenolic acids biosynthesis in Salvia miltiorrhiza. Ind Crop Prod. 2018;124:402–11. https://doi.org/10.1016/j.indcrop.2018.07.046.

 

Yang N, Zhou WP, Su J, Wang XF, Li L, Wang LR, Cao XY, Wang ZZ. Overexpression of SmMYC2 increases the production of phenolic acids in Salvia miltiorrhiza. Front Plant Sci. 2017;8:1804. https://doi.org/10.3389/fpls.2017.01804.

 

Yao L, Wang J, Sun JC, He JP, Paek KY, Park SY, Huang LQ, Gao WY. A WRKY transcription factor, PgWRKY4X, positively regulates ginsenoside biosynthesis by activating squalene epoxidase transcription in Panax ginseng. Ind Crop Prod. 2020;154:112671. https://doi.org/10.1016/j.indcrop.2020.112671.

 

Ye JB, Zhang X, Tan JP, Xu F, Cheng SY, Chen ZX, Zhang WW, Liao YL. Global identification of Ginkgo biloba microRNAs and insight into their role in metabolism regulatory network of terpene trilactones by high-throughput sequencing and degradome analysis. Ind Crop Prod. 2020;148:112289. https://doi.org/10.1016/j.indcrop.2020.112289.

 

Yin J, Li X, Zhan YG, Li Y, Qu ZY, Sun L, Wang SY, Yang J, Xiao JL. Cloning and expression of BpMYC4 and BpbHLH9 genes and the role of BpbHLH9 in triterpenoid synthesis in birch. BMC Plant Biol. 2017;17(1):214. https://doi.org/10.1186/s12870-017-1150-z.

 

Ying S, Zhang DF, Fu J, Shi YS, Song YC, Wang TY, Li Y. Cloning and characterization of a maize bZIP transcription factor, ZmbZIP72, confers drought and salt tolerance in transgenic Arabidopsis. Planta. 2012;235(2):253–66. https://doi.org/10.1007/s00425-011-1496-7.

 

Yu ZX, Li JX, Yang CQ, Hu WL, Wang LJ, Chen XY. The jasmonate-responsive AP2/ERF transcription factors AaERF1 and AaERF2 positively regulate artemisinin biosynthesis in Artemisia annua L. Mol plant. 2012;5(2):353–65. https://doi.org/10.1093/mp/ssr087.

 

Zhang F, Fu X, Lv Z, Lu X, Shen Q, Zhang L, Zhu MM, Wang GF, Sun XF, Liao ZH, Tang KX. A basic leucine zipper transcription factor, AabZIP1, connects abscisic acid signaling with artemisinin biosynthesis in Artemisia annua. Mol Plant. 2015;8(1):163–75. https://doi.org/10.1016/j.molp.2014.12.004.

 

Zhang HM, Lang Z, Zhu JK. Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol. 2018;19:489–506. https://doi.org/10.1038/s41580-018-0016-z.

 

Zhang HT, Hedhili S, Montiel G, Zhang YX, Chatel G, Pré M, Gantet P, Memelink J. The basic helix-loop-helix transcription factor CrMYC2 controls the jasmonate-responsive expression of the ORCA genes that regulate alkaloid biosynthesis in Catharanthus roseus. Plant J. 2011;67(1):61–71. https://doi.org/10.1111/j.1365-313X.2011.04575.x.

 

Zhang KP, Wang NH, Gao XQ, Ma Q. Integrated metabolite profiling and transcriptome analysis reveals tissue-specific regulation of terpenoid biosynthesis in Artemisia argyi. Genomics. 2022;114(4):110388. https://doi.org/10.1016/j.ygeno.2022.110388.

 

Zhang Q, Zhou W, Li B, Li L, Fu M, Zhou L, Yu XD, Wang DH, Wang ZZ. Genome-wide analysis and the expression pattern of the ERF gene family in Hypericum perforatum. Plants. 2021;10(1):133. https://doi.org/10.3390/plants10010133.

 

Zhang ST, Zhu C, Lyu YM, Chen Y, Zhang ZH, Lai ZX, Lin YL. Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour. BMC Genomics. 2020;21:62. https://doi.org/10.1186/s12864-020-6469-4.

 

Zhang WW, Xu F, Cheng SY, Liao YL. Characterization and functional analysis of a MYB gene (GbMYBFL) related to flavonoid accumulation in Ginkgo biloba. Genes Genomics. 2018;40(1):49–61. https://doi.org/10.1007/s13258-017-0609-5.

 

Zhang X, Ge F, Deng B, Shah T, Huang ZJ, Liu DQ, Chen CY. Molecular cloning and characterization of PnbHLH1 transcription factor in Panax notoginseng. Molecules. 2017;22(8). https://doi.org/10.3390/molecules22081268.

 

Zhang X, Luo HM, Xu ZC, Zhu YJ, Ji AJ, Song JY, Chen SL. Genome-wide characterisation and analysis of bHLH transcription factors related to tanshinone biosynthesis in Salvia miltiorrhiza. Sci Rep. 2015;5:11244. https://doi.org/10.1038/srep11244.

 

Zhang Y, Xu ZC, Ji AJ, Luo HM, Song JM. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza. Acta Pharm Sin B. 2018;8(2):295–305. https://doi.org/10.1016/j.apsb.2017.09.002.

 

Zhang Y, Ji AJ, Xu ZC. Luo HM, Song JY. The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza. Plant Mol Biol. 2019;100:83–93. https://doi.org/10.1007/s11103-019-00845-7.

 

Zhang YQ, Zheng S, Liu ZJ, Wang LG, Bi YR. Both HY5 and HYH are necessary regulators for low temperature-induced anthocyanin accumulation in Arabidopsis seedlings. J Plant Physiol. 2011;168(4):367–74. https://doi.org/10.1016/j.jplph.2010.07.025.

 

Zhao SQ, Wang XW, Yan XM, Guo LX, Mi XZ, Xu QS, Zhu JY, Wu AL, Liu LL, Wei CL. Revealing of MicroRNA involved regulatory gene networks on terpenoid biosynthesis in Camellia sinensis in different growing time points. J Agric Food Chem. 2018;66(47):12604–16. https://doi.org/10.1021/acs.jafc.8b05345.

 

Zhao T, Zhan ZP, Jiang DH. Histone modifications and their regulatory roles in plant development and environmental memory. J Genet Genomics. 2019;46(10):467–76. https://doi.org/10.1016/j.jgg.2019.09.005.

 

Zhao Y, Zhang GH, Tang QY, Song WL, Gao QQ, Xiang GS, Li X, Liu GZ, Fan W, Li XN, Yang SC, Zhai CX. EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus. Front Plant Sci. 2022;13:946827. https://doi.org/10.3389/fpls.2022.946827.

 

Zheng H, Fu X, Shao J, Tang Y, Yu M, Li L, Huang LQ, Tang KX. Transcriptional regulatory network of high-value active ingredients in medicinal plants. Trends Plant Sci. 2023; S1360-1385. https://doi.org/10.1016/j.tplants.2022.12.007.

 

Zheng LL, Qiu BL, Su LL, Wang HL, Cui XM, Ge F, Liu DQ. Panax notoginseng WRKY transcription factor 9 is a positive regulator in responding to Root Rot pathogen Fusarium solani. Front Plant Sci. 2022;13:930644. https://doi.org/10.3389/fpls.2022.930644.

 

Zhong Y, Xun WB, Wang XH, Tian SW, Zhang YC, Li DW, Zhou Y, Qin YX, Zhang B, Zhao GW, Cheng X, Liu YG, Chen HM, Li LG, Osbourn A, Lucas WJ, Huang SW, Ma YS, Shang Y. Root-secreted bitter triterpene modulates the rhizosphere microbiota to improve plant fitness. Nat Plants. 2022;8:887–96. https://doi.org/10.1038/s41477-022-01201-2.

 

Zhong YJ, Li L, Hao XL, Fu XQ, Ma YN, Xie LH, Shen Q, Pan QF, Sun XF, Tang KX. AaABF3, an abscisic acid-responsive transcription factor, positively regulates artemisinin biosynthesis in Artemisia annua. Front Plant Sci. 2018;9:1777. https://doi.org/10.3389/fpls.2018.01777.

 

Zhou W, Shi M, Deng CP, Lu SJ, Huang FF, Wang Y, Kai GY. The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza. Hortic Res. 2021;8(1):10. https://doi.org/10.1038/s41438-020-00443-5.

 

Zhou X, Liao YL, Kim SU, Chen ZX, Nie GP, Cheng SY, Ye JB, Xu F. Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba. Sci Rep. 2020;10(1):13723. https://doi.org/10.1038/s41598-020-69305-3.

 

Zhu X, Liu X, Liu T, Wang Y, Ahmed N, Li Z, Jiang H. Synthetic biology of plant natural products: From pathway elucidation to engineered biosynthesis in plant cells. Plant Commun. 2021; 2(5),100229.https://doi.org/10.1016/j.xplc.2021.100229.

Molecular Horticulture
Pages 11-11
Cite this article:
Zhao Y, Liu G, Yang F, et al. Multilayered regulation of secondary metabolism in medicinal plants. Molecular Horticulture, 2023, 3(2): 11. https://doi.org/10.1186/s43897-023-00059-y

134

Views

3

Downloads

22

Crossref

16

Web of Science

13

Scopus

Altmetrics

Received: 28 March 2023
Accepted: 27 April 2023
Published: 06 June 2023
© The Author(s) 2023.

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Return