| [1] |
Dai LX, Miao X, Yang XR, Zuo LP, Lan ZH, et al. 2022. High value-added application of two renewable sources as healthy food: the nutritional properties, chemical compositions, antioxidant, and antiinflammatory activities of the stalks of Rheum officinale baill. and Rheum tanguticum maxim. ex regel. Frontiers in Nutrition 8:770264 doi: 10.3389/fnut.2021.770264 |
| [2] |
Zhao X, Yan F, Li YM, Tang J, Hu XC, et al. 2024. Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. Chinese Medicine 19:23 doi: 10.1186/s13020-024-00891-4 |
| [3] |
Tian Y, Ma B, Yu S, Li Y, Pei H, et al. 2023. Clinical antitumor application and pharmacological mechanisms of Dahuang Zhechong Pill. Chinese Herbal Medicines 15:169−80 doi: 10.1016/j.chmed.2023.02.002 |
| [4] |
Shang XF, Zhao ZM, Li JC, Yang GZ, Liu YQ, et al. 2019. Insecticidal and antifungal activities of Rheum palmatum L. anthraquinones and structurally related compounds. Industrial Crops and Products 137:508−20 doi: 10.1016/j.indcrop.2019.05.055 |
| [5] |
Huang A, Deng W, Li X, Zheng Q, Wang X, et al. 2022. Long-chain alkanol–alkyl carboxylic acid-based low-viscosity hydrophobic deep eutectic solvents for one-pot extraction of anthraquinones from Rhei Radix et Rhizoma. Journal of Pharmaceutical Analysis 12:87−95 doi: 10.1016/j.jpha.2021.03.002 |
| [6] |
Yao M, Li J, He M, Ouyang H, Ruan L, et al. 2021. Investigation and identification of the multiple components of Rheum officinale Baill. using ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight tandem mass spectrometry and data mining strategy. Journal of Separation Science 44:681−90 doi: 10.1002/jssc.202000735 |
| [7] |
Gao LL, Guo T, Xu XD, Yang JS. 2017. Rapid identification and simultaneous analysis of multiple constituents from Rheum tanguticum Maxim. ex Balf. by UPLC/Q-TOF-MS. Natural Product Research 31:1529−35 doi: 10.1080/14786419.2017.1280491 |
| [8] |
Yuan W, Wang QF, Pei WH, Li SY, Wang TM, et al. 2024. Age-induced changes in ginsenoside accumulation and primary metabolic characteristics of Panax ginseng in transplantation mode. Journal of Ginseng Research 48:103−11 doi: 10.1016/j.jgr.2023.09.003 |
| [9] |
Zhao S, Xiong F, Li J, Ye Z, Wang L, et al. 2024. Metabolomic characteristics and anthraquinones accumulation patterns of Rhubarb in different tissues and roots from different developmental stages. Food Bioscience 62:105426 doi: 10.1016/j.fbio.2024.105426 |
| [10] |
Yan S, Zhao TM, Zhang XQ, Xing JY, Hu YD, et al. 2018. Comparison of polysaccharide and dendrobine content in Hejiang Dendrobium nobile at different harvesting time. China Pharmacy 29(1):73−77 doi: 10.6039/j.issn.1001-0408.2018.01.19 |
| [11] |
Zheng QX, Wu HF, Guo J, Nan HJ, Chen SL, et al. 2013. Review of rhubarbs: chemistry and pharmacology. Chinese Herbal Medicines 5:9−32 doi: 10.7501/j.issn.1674-6384.2013.01.003 |
| [12] |
Si C, Zeng D, Yu Z, Teixeira da Silva JA, Duan J, et al. 2022. Transcriptomic and metabolomic analyses reveal the main metabolites in Dendrobium officinale leaves during the harvesting period. Plant Physiology and Biochemistry 190:24−34 doi: 10.1016/j.plaphy.2022.08.026 |
| [13] |
Cui Y, Wang Z, Chen S, Vainstein A, Ma H. 2019. Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.). BMC Plant Biology 19:146 doi: 10.1186/s12870-019-1742-x |
| [14] |
Wang M, Wang X, Xu H, Liu X, Bi Q, et al. 2022. Integrated transcriptomics and metabolomics analysis to characterize the optimal picking time in yellowhorn (Xanthoceras sorbifolium) flowers. Industrial Crops and Products 187:115389 doi: 10.1016/j.indcrop.2022.115389 |
| [15] |
Yuan Y, Zuo J, Zhang H, Zu M, Liu S. 2022. Analysis of the different growth years accumulation of flavonoids in Dendrobium moniliforme (L.) Sw. by the integration of metabolomic and transcriptomic approaches. Frontiers in Nutrition 9:928074 doi: 10.3389/fnut.2022.928074 |
| [16] |
Wang H, Asker K, Zhan C, Wang N. 2021. Transcriptomic and metabolic analysis of fruit development and identification of genes involved in raffinose and hydrolysable tannin biosynthesis in walnuts. Journal of Agricultural and Food Chemistry 69:8050−62 doi: 10.1021/acs.jafc.1c02434 |
| [17] |
Liu Y, Tang N, Lin D, Deng W, Li Z. 2023. Integration of multi-omics analyses highlights the secondary metabolism response of tomato fruit to low temperature storage. Food Research International 173:113316 doi: 10.1016/j.foodres.2023.113316 |
| [18] |
Schubert M, Lindgreen S, Orlando L. 2016. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes 9:88 doi: 10.1186/s13104-016-1900-2 |
| [19] |
Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323 doi: 10.1186/1471-2105-12-323 |
| [20] |
Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550 doi: 10.1186/s13059-014-0550-8 |
| [21] |
Du MF, Ding GJ. 2018. Analysis of SSR loci of functional gene linked to drought resistance based on transcriptome sequences in Pinus massoniana under drought stress. Forest Research 31:9−19 doi: 10.13275/j.cnki.lykxyj.2018.05.002 |
| [22] |
Kumar L, Futschik ME. 2007. Mfuzz: a software package for soft clustering of microarray data. Bioinformation 2:5−7 doi: 10.6026/97320630002005 |
| [23] |
Tang J, Kong D, Cui Q, Wang K, Zhang D, et al. 2018. Prognostic genes of breast cancer identified by gene co-expression network analysis. Frontiers in Oncology 8:374 doi: 10.3389/fonc.2018.00374 |
| [24] |
Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. 2019. Cytoscape StringApp: network analysis and visualization of proteomics data. Journal of Proteome Research 18:623−32 doi: 10.1021/acs.jproteome.8b00702 |
| [25] |
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498−504 doi: 10.1101/gr.1239303 |
| [26] |
Tian T, Liu Y, Yan H, You Q, Yi X, et al. 2017. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research 45:W122−W129 doi: 10.1093/nar/gkx382 |
| [27] |
Xie C, Mao X, Huang J, Ding Y, Wu J, et al. 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research 39:W316−W322 doi: 10.1093/nar/gkr483 |
| [28] |
Son SM, Moon KD, Lee CY. 2000. Rhubarb juice as a natural antibrowning agent. Journal of Food Science 65:1288−89 doi: 10.1111/j.1365-2621.2000.tb10598.x |
| [29] |
Shahrajabian MH, Cheng Q, Sun W. 2022. Wonderful natural drugs with surprising nutritional values, Rheum species, gifts of the nature. Letters in Organic Chemistry 19:818−26 doi: 10.2174/1570178619666220112115918 |
| [30] |
Zheng X, Xiao H, Chen J, Zhu J, Fu Y, et al. 2022. Metabolome and whole-transcriptome analyses reveal the molecular mechanisms underlying hypoglycemic nutrient metabolites biosynthesis in Cyclocarya paliurus leaves during different harvest stages. Frontiers in Nutrition 9:851569 doi: 10.3389/fnut.2022.851569 |
| [31] |
Li Y, Kong D, Fu Y, Sussman MR, Wu H. 2020. The effect of developmental and environmental factors on secondary metabolites in medicinal plants. Plant Physiology and Biochemistry 148:80−89 doi: 10.1016/j.plaphy.2020.01.006 |
| [32] |
Yin L, Cai Z, Zhu B, Xu C. 2018. Identification of key pathways and genes in the dynamic progression of HCC based on WGCNA. Genes 9:92 doi: 10.3390/genes9020092 |
| [33] |
Xu L, Cao M, Wang Q, Xu J, Liu C, et al. 2022. Insights into the plateau adaptation of Salvia castanea by comparative genomic and WGCNA analyses. Journal of Advanced Research 42:221−35 doi: 10.1016/j.jare.2022.02.004 |
| [34] |
Eljounaidi K, Cankar K, Comino C, Moglia A, Hehn A, et al. 2014. Cytochrome P450s from Cynara cardunculus L. CYP71AV9 and CYP71BL5, catalyze distinct hydroxylations in the sesquiterpene lactone biosynthetic pathway. Plant Science 223:59−68 doi: 10.1016/j.plantsci.2014.03.007 |
| [35] |
Li C, Wu J, Hu KD, Wei SW, Sun HY, et al. 2020. PyWRKY26 and PybHLH3 cotargeted the PyMYB114 promoter to regulate anthocyanin biosynthesis and transport in red-skinned pears. Horticulture Research 7:37 doi: 10.1038/s41438-020-0254-z |
| [36] |
Cong L, Qu Y, Sha G, Zhang S, Ma Y, et al. 2021. PbWRKY75 promotes anthocyanin synthesis by activating PbDFR, PbUFGT, and PbMYB10b in pear. Physiologia Plantarum 173:1841−49 doi: 10.1111/ppl.13525 |
| [37] |
Öztürk M, Aydoğmuş-Öztürk F, Duru ME, Topçu G. 2007. Antioxidant activity of stem and root extracts of Rhubarb (Rheum ribes): an edible medicinal plant. Food Chemistry 103:623−30 doi: 10.1016/j.foodchem.2006.09.005 |
| [38] |
Tabin S, Gupta R, Kamili A, Parray J. 2022. Medical and medicinal importance of Rheum spp. collected from different altitudes of the Kashmir Himalayan range. Cellular, Molecular and Biomedical Reports 2:187−201 doi: 10.55705/cmbr.2022.349901.1050 |
| [39] |
Li Y, Jiang JG. 2018. Health functions and structure–activity relationships of natural anthraquinones from plants. Food & Function 9(12):6063−80 doi: 10.1039/C8FO01569D |
| [40] |
Berillo D, Kozhahmetova M, Lebedeva L. 2022. Overview of the biological activity of anthraquinons and flavanoids of the plant Rumex species. Molecules 27:1204 doi: 10.3390/molecules27041204 |
| [41] |
Liao H, Quan H, Huang B, Ji H, Zhang T, et al. 2023. Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata. Phytochemistry 214:113831 doi: 10.1016/j.phytochem.2023.113831 |
| [42] |
Cui Y, Gao X, Wang J, Shang Z, Zhang Z, et al. 2021. Full-length transcriptome analysis reveals candidate genes involved in terpenoid biosynthesis in Artemisia argyi. Frontiers in Genetics 12:659962 doi: 10.3389/fgene.2021.659962 |
| [43] |
Zhang H, He Q, Xing L, Wang R, Wang Y, et al. 2024. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. Plant Communications 5:100677 doi: 10.1016/j.xplc.2023.100677 |
| [44] |
Alami MM, Guo S, Mei Z, Yang G, Wang X. 2024. Environmental factors on secondary metabolism in medicinal plants: exploring accelerating factors. Medicinal Plant Biology 3:e016 doi: 10.48130/mpb-0024-0016 |
| [45] |
Zhou L, Sun J, Zhang T, Tang Y, Liu J, et al. 2022. Comparative transcriptome analyses of different Rheum officinale tissues reveal differentially expressed genes associated with anthraquinone, catechin, and Gallic acid biosynthesis. Genes 13:1592 doi: 10.3390/genes13091592 |
| [46] |
Hu Y, Zhang H, Sun J, Li W, Li Y. 2022. Comparative transcriptome analysis of different tissues of Rheum tanguticum Maxim. ex Balf. (Polygonaceae) reveals putative genes involved in anthraquinone biosynthesis. Genetics and Molecular Biology 45:e20210407 doi: 10.1590/1678-4685-GMB-2021-0407 |
| [47] |
Li Y, Wang Z, Zhu M, Niu Z, Li M, et al. 2023. A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis. Communications Biology 6:867 doi: 10.1038/s42003-023-05248-5 |