[1]

Mei XD, Cao YF, Che YY, Li J, Shang ZP, et al. 2019. Danshen: a phytochemical and pharmacological overview. Chinese Journal of Natural Medicines 17:59−80

doi: 10.1016/S1875-5364(19)30010-X
[2]

Jiang Z, Gao W, Huang L. 2019. Tanshinones, Critical Pharmacological Components in Salvia miltiorrhiza. Frontiers in Pharmacology 10:202

doi: 10.3389/fphar.2019.00202
[3]

Zheng H, Fu X, Shao J, Tang Y, Yu M, et al. 2023. Transcriptional regulatory network of high-value active ingredients in medicinal plants. Trends in Plant Science 28(4):429−46

doi: 10.1016/j.tplants.2022.12.007
[4]

Zheng H, Jing L, Jiang X, Pu C, Zhao S, et al. 2021. The ERF-VII transcription factor SmERF73 coordinately regulates tanshinone biosynthesis in response to stress elicitors in Salvia miltiorrhiza. New Phytologist 231:1940−55

doi: 10.1111/nph.17463
[5]

Howe GA, Major IT, Koo AJ. 2018. Modularity in jasmonate signaling for multistress resilience. Annual Review of Plant Biology 69:387−415

doi: 10.1146/annurev-arplant-042817-040047
[6]

Zhou Y, Sun W, Chen J, Tan H, Xiao Y, et al. 2016. SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza. Scientific Reports 6:22852

doi: 10.1038/srep22852
[7]

Du T, Niu J, Su J, Li S, Guo X, et al. 2018. SmbHLH37 functions antagonistically with SmMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza. Frontiers in Plant Science 9:1720

doi: 10.3389/fpls.2018.01720
[8]

Ma P, Pei T, Lv B, Wang M, Dong J, et al. 2022. Functional pleiotropism, diversity, and redundancy of Salvia miltiorrhiza Bunge JAZ family proteins in jasmonate-induced tanshinone and phenolic acid biosynthesis. Horticulture Research 9:uhac166

doi: 10.1093/hr/uhac166
[9]

Fu X, Peng B, Hassani D, Xie L, Liu H, et al. 2021. AaWRKY9 contributes to light- and jasmonate-mediated to regulate the biosynthesis of artemisinin in Artemisia annua. New Phytologist 231:1858−74

doi: 10.1111/nph.17453
[10]

Yi R, Yan J, Xie D. 2020. Light promotes jasmonate biosynthesis to regulate photomorphogenesis in Arabidopsis. Science China Life Sciences 63:943−52

doi: 10.1007/s11427-019-1584-4
[11]

Alallaq S, Ranjan A, Brunoni F, Novák O, Lakehal A, et al. 2020. Light controls de novo adventitious root regeneration by modulating jasmonate and cytokinin homeostasis in Norway spruce hypocotyls. bioRxiv Preprint

doi: 10.1101/2020.03.11.985838
[12]

Wang Y, Fan X, Lin F, He G, Terzaghi W, et al. 2014. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proceedings of the National Academy of Sciences of the United States of America 111:10359−64

doi: 10.1073/pnas.1409457111
[13]

Feng S, Wang R, Gu W, Yu B, Wang Y, et al. 2019. Effects of red light and blue light on root morphology and accumulation of bioactive compounds in Salvia miltiorrhiza. Chinese Traditional and Herbal Drugs 50:5313−18

doi: 10.7501/j.issn.0253-2670.2019.21.026
[14]

Liang Z, Li Q, Xu W. 2012. Effects of different light quality on growth, active ingredients and enzyme activities of Salvia miltiorrhiza. China Journal of Chinese Materia Medica 37:2055−60

doi: 10.4268/cjcmm20121405
[15]

Svyatyna K, Jikumaru Y, Brendel R, Reichelt M, MithÖFer A, et al. 2013. Light induces jasmonate‐isoleucine conjugation via OsJAR1‐dependent and ‐independent pathways in rice. Plant, Cell & Environment 37:827−39

doi: 10.1111/pce.12201
[16]

Ortigosa A, Fonseca S, Franco‐Zorrilla JM, Fernández‐Calvo P, Zander M, et al. 2020. The JA‐pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression. The Plant Journal 102:138−52

doi: 10.1111/tpj.14618
[17]

Gangappa SN, Botto JF. 2016. The Multifaceted Roles of HY5 in Plant Growth and Development. Molecular Plant 9:1353−65

doi: 10.1016/j.molp.2016.07.002
[18]

Shin J, Park E, Choi G. 2007. PIF3 regulates anthocyanin biosynthesis in an HY5-dependent manner with both factors directly binding anthocyanin biosynthetic gene promoters in Arabidopsis. The Plant Journal 49:981−94

doi: 10.1111/j.1365-313X.2006.03021.x
[19]

Hao X, Zhong Y, Nützmann HW, Fu X, Yan T, et al. 2019. Light-Induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annual. Plant and Cell Physiology 60:1747−60

doi: 10.1093/pcp/pcz084
[20]

Zhou F, Sun T, Zhao L, Pan X, Lu S. 2015. The bZIP transcription factor HY5 interacts with the promoter of the monoterpene synthase gene QH6 in modulating its rhythmic expression. Frontiers in plant science 6:304

doi: 10.3389/fpls.2015.00304
[21]

Gangappa SN, Botto JF. 2014. The BBX family of plant transcription factors. Trends in Plant Science 19:460−70

doi: 10.1016/j.tplants.2014.01.010
[22]

Bursch K, Toledo-Ortiz G, Pireyre M, Lohr M, Braatz C, et al. 2020. Identification of BBX proteins as rate-limiting cofactors of HY5. Nature Plants 6:921−28

doi: 10.1038/s41477-020-0725-0
[23]

Bai S, Tao R, Yin L, Ni J, Yang Q, et al. 2019. Two B-box proteins, PpBBX18 and PpBBX21, antagonistically regulate anthocyanin biosynthesis via competitive association with Pyrus pyrifolia ELONGATED HYPOCOTYL 5 in the peel of pear fruit. The Plant Journal 100:1208−23

doi: 10.1111/tpj.14510
[24]

Bai B, Lu N, Li Y, Guo S, Yin H, et al. 2019. OsBBX14 promotes photomorphogenesis in rice by activating OsHY5L1 expression under blue light conditions. Plant Science 284:192−202

doi: 10.1016/j.plantsci.2019.04.017
[25]

Zhao X, Heng Y, Wang X, Deng X, Xu D. 2020. A positive feedback loop of BBX11-BBX21-HY5 promotes photomorphogenic development in Arabidopsis. Plant Communications 1:100045

doi: 10.1016/j.xplc.2020.100045
[26]

Xu D, Gao S, Ma Y, Wang X, Feng L, et al. 2017. The G-Protein β subunit AGB1 promotes hypocotyl elongation through inhibiting transcription activation function of BBX21 in Arabidopsis. Molecular Plant 10:1206−23

doi: 10.1016/j.molp.2017.08.004
[27]

Xu D, Li J, Gangappa SN, Hettiarachchi C, Lin F, et al. 2014. Convergence of light and ABA signaling on the ABI5 promoter. Plos Genetics 10:e1004197

doi: 10.1371/journal.pgen.1004197
[28]

Chen H, Zhang J, Neff MM, Hong S, Zhang H, et al. 2008. Integration of light and abscisic acid signaling during seed germination and early seedling development. Proceedings of the National Academy of Sciences of the United States of America 105:4495−500

doi: 10.1073/pnas.0710778105
[29]

Wang F, Zhang L, Chen X, Wu X, Xiang X, et al. 2018. SlHY5 integrates temperature, light and hormone signaling to balance plant growth and cold tolerance. Plant Physiology 179:749−60

doi: 10.1104/pp.18.01140
[30]

Weller JL, Hecht V, Vander Schoor JK, Davidson SE, Ross JJ. 2009. Light regulation of gibberellin biosynthesis in Pea is mediated through the COP1/HY5 pathway. The Plant Cell 21:800−13

doi: 10.1105/tpc.108.063628
[31]

Fan XY, Sun Y, Cao DM, Bai MY, Luo XM, et al. 2012. BZS1, a B-box protein, promotes photomorphogenesis downstream of both brassinosteroid and light signaling pathways. Molecular Plant 5:591−600

doi: 10.1093/mp/sss041
[32]

Ma Y, Cui G, Chen T, Ma X, Wang R, et al. 2021. Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza. Nature Communications 12:685

doi: 10.1038/s41467-021-20959-1
[33]

Li CY, Yang L, Liu Y, Xu ZG, Gao J, et al. 2022. The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants. Cell Reports 40:111236

doi: 10.1016/j.celrep.2022.111236
[34]

Cao W, Wang Y, Shi M, Hao X, Zhao W, et al. 2018. Transcription factor SmWRKY1 positively promotes the biosynthesis of tanshinones in Salvia miltiorrhiza. Frontiers in Plant Science 9:554

doi: 10.3389/fpls.2018.00554
[35]

Zhang C, Xing B, Yang D, Ren M, Guo H, et al. 2020. SmbHLH3 acts as a transcription repressor for both phenolic acids and tanshinone biosynthesis in Salvia miltiorrhiza hairy roots. Phytochemistry 169:112183

doi: 10.1016/j.phytochem.2019.112183
[36]

Zhou L, Huang Y, Wang Q, Guo D. 2021. AaHY5 ChIP-seq based on transient expression system reveals the role of AaWRKY14 in artemisinin biosynthetic gene regulation. Plant Physiology and Biochemistry 168:321−28

doi: 10.1016/j.plaphy.2021.10.010
[37]

Deng C, Shi M, Fu R, Zhang Y, Wang Q, et al. 2020. ABA-responsive transcription factor bZIP1 is involved in modulating biosynthesis of phenolic acids and tanshinones in Salvia miltiorrhiza. Journal of Experimental Botany 71:5948−62

doi: 10.1093/jxb/eraa295
[38]

Yang G, Zhang C, Dong H, Liu X, Guo H, et al. 2022. Activation and negative feedback regulation of SlHY5 transcription by the SlBBX20/21–SlHY5 transcription factor module in UV-B signaling. The Plant Cell 34:2038−55

doi: 10.1093/plcell/koac064
[39]

Li Y, Tong Y, Ye J, Zhang C, Li B, et al. 2023. Genome-Wide characterization of B-Box gene family in Salvia miltiorrhiza. International Journal of Molecular Sciences 24:2146

doi: 10.3390/ijms24032146
[40]

Wei C, Chien C, Ai L, Zhao J, Zhang Z, et al. 2016. The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis. Journal of Genetics and Genomics 43:555−63

doi: 10.1016/j.jgg.2016.05.007
[41]

Xu D, Jiang Y, Li J, Lin F, Holm M, et al. 2016. BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation. Proceedings of the National Academy of Sciences of the United States of America 113:7655−60

doi: 10.1073/pnas.1607687113
[42]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923−30

doi: 10.1093/bioinformatics/btt656
[43]

Wang L, Feng Z, Wang X, Wang X, Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136−38

doi: 10.1093/bioinformatics/btp612
[44]

Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P. 2010. Inferring regulatory networks from expression data using tree-based methods. Plos One 5:e12776

doi: 10.1371/journal.pone.0012776
[45]

Chen K, Liu J, Ji R, Chen T, Zhou X, et al. 2019. Biogenic synthesis and spatial distribution of endogenous phytohormones and ginsenosides provide insights on their intrinsic relevance in Panax ginseng. Frontiers in Plant Science 9:1951

doi: 10.3389/fpls.2018.01951
[46]

Frey F. 2017. SPSS (Software). In The International Encyclopedia of Communication Research Methods, eds. Matthes J, Davis CS, Potter RF. Los Angeles, USA: John Wiley & Sons. pp. 1−2. https://doi.org/10.1002/9781118901731.iecrm0237

[47]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCᴛ method. Methods 25:402−08

doi: 10.1006/meth.2001.1262