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Lyu X, Chen Y, Gao S, Cao W, Fan D, Duan Z, Xia Z. Metabolomic and transcriptomic analysis of cold plasma promoting biosynthesis of active substances in broccoli sprouts. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:925-937. [PMID: 37443417 DOI: 10.1002/pca.3256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
INTRODUCTION Broccoli sprouts have great health and commercial value because they are rich in sulforaphane, a special bioactive compound that helps to prevent chronic diseases, such as cancer and cardiovascular disease. OBJECTIVE The aim of this study was to increase the levels of active substances in broccoli sprouts and understand their metabolic mechanisms. METHODOLOGY Metabolomics based on liquid chromatography-tandem mass spectrometry and transcriptome analysis were combined to analyse the enrichment of metabolites in broccoli sprouts treated with cold plasma. RESULTS After 2 min of cold plasma treatment, the contents of sulforaphane, glucosinolates, total phenols, and flavonoids, as well as myrosinase activity, were greatly improved. Transcriptomics revealed 7460 differentially expressed genes in the untreated and treated sprouts. Metabolomics detected 6739 differential metabolites, including most amino acids, their derivatives, and organic acids. Enrichment analyses of metabolomics and transcriptomics identified the 20 most significantly differentially expressed metabolic pathways. CONCLUSIONS Overall, cold plasma treatment can induce changes in the expression and regulation of certain metabolites and genes encoding active substances in broccoli sprouts.
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Affiliation(s)
- Xingang Lyu
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Yi Chen
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Shiwei Gao
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Wei Cao
- College of Food Science and Technology, Northwest University, Xi'an, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, Shaanxi, China
| | - Zhiguang Duan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, Shaanxi, China
| | - Zengrun Xia
- Ankang R&D Center for Se-enriched Products, Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, Ankang, Shaanxi, China
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Ma R, Sun X, Yang C, Fan Y. Integrated transcriptome and metabolome provide insight into flavonoid variation in goji berries (Lycium barbarum L.) from different areas in China. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107722. [PMID: 37150012 DOI: 10.1016/j.plaphy.2023.107722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/17/2023] [Accepted: 04/25/2023] [Indexed: 05/09/2023]
Abstract
Goji berries (Lycium barbarum L.) were rich in flavonoids, showing high nutritional and medicinal value. However, a thorough evaluation and comparison of the flavonoids in goji berries from various regions and the possible biological regulation pathways with differences are scanty. Here, we investigated the flavonoid metabolites and gene expression levels of goji berries from three major production areas in China using transcriptomics sequencing and metabolomics. The total flavonoid content and total polyphenol content of goji berry in Ningxia (57.87 μg/g and 183.41 μg/g, respectively) were higher than in Qinghai (50.77 μg/g and 156.81 μg/g) and Gansu (47.86 μg/g and 111.17 μg/g). We identified the 105 differentially accumulated flavonoids (DAFs) and 1858 differentially expressed genes (DEGs) from the goji berries in three habitats. Interestingly, gossypetin-3-O-rutinoside and isorhamnetin were significantly expressed between Ningxia and Qinghai berries. The chalcone isomerase (CHI), chalcone synthase (CHS), and flavonol synthase (FLS) genes also played key roles in the regulation of flavonoid synthesis. In addition, MYB1 positively regulated the expression of quercetin-3-O-glucoside, quercetin-7-O-glucoside and isohyperoside. As a result, we speculated that CHI, CHS, FLS genes, and related transcription factors jointly controlled the variation of flavone accumulation in goji berries. These findings may provide a new perspective for understanding the accumulation and molecular mechanisms of goji flavonoids.
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Affiliation(s)
- Ruixue Ma
- School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, Ningxia, PR China
| | - Xiazhi Sun
- School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, Ningxia, PR China
| | - Chao Yang
- School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, Ningxia, PR China
| | - Yanli Fan
- School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, Ningxia, PR China.
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Luo Y, Deng M, Zhang X, Zhang D, Cai W, Long Y, Xiong X, Li Y. Integrative Transcriptomic and Metabolomic Analysis Reveals the Molecular Mechanism of Red Maple ( Acer rubrum L.) Leaf Coloring. Metabolites 2023; 13:metabo13040464. [PMID: 37110123 PMCID: PMC10143518 DOI: 10.3390/metabo13040464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
This study employed a combination of ultraviolet spectrophotometry, LC-ESI-MS/MS system, and RNA-sequencing technology; the extracts and isolation of total RNA from the red and yellow leaf strains of red maple (Acer rubrum L.) at different developmental stages were subjected to an intercomparison of the dynamic content of chlorophyll and total anthocyanin, flavonoid metabolite fingerprinting, and gene expression. The metabonomic results indicated that one hundred and ninety-two flavonoids were identified, which could be classified into eight categories in the red maple leaves. Among them, 39% and 19% were flavones and flavonols, respectively. The metabolomic analysis identified 23, 32, 24, 24, 38, and 41 DAMs in the AR1018r vs. AR1031r comparison, the AR1018r vs. AR1119r comparison, the AR1031r vs. AR1119r comparison, the AR1018y vs. AR1031y comparison, the AR1018y vs. AR1119y comparison, and the AR1031y vs. AR1119y comparison, respectively. In total, 6003 and 8888 DEGs were identified in AR1018r vs. AR1031r comparison and in the AR1018y vs. AR1031y comparison, respectively. The GO and KEGG analyses showed that the DEGs were mainly involved in plant hormone signal transduction, flavonoid biosynthesis, and other metabolite metabolic processes. The comprehensive analysis revealed that caffeoyl-CoA 3-O-methyltransferase (Cluster-28704.45358 and Cluster-28704.50421) was up-regulated in the red strain but down-regulated in the yellow strain, while Peonidin 3-O-glucoside chloride and Pelargonidin 3-O-beta-D-glucoside were up-regulated in both the red and yellow strains. By successfully integrating the analyses on the behavior of pigment accumulation, dynamics of flavonoids, and differentially expressed genes with omics tools, the regulation mechanisms underlying leaf coloring in red maple at the transcriptomic and metabolomic levels were demonstrated, and the results provide valuable information for further research on gene function in red maple.
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Affiliation(s)
- Yuanyuan Luo
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- College of Oriental Science & Technology, Hunan Agricultural University, Changsha 410128, China
| | - Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xia Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Damao Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Wenqi Cai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Yuelin Long
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- College of Landscape Architecture and Art Design, Hunan Agricultural University, Changsha 410128, China
| | - Xingyao Xiong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yanlin Li
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Kunpeng Institute of Modern Agriculture, Foshan 528200, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Li C, Chen L, Fan Q, He P, Wang C, Huang H, Huang R, Tang J, Tadda SA, Qiu D, Qiu Z. Weighted Gene Co-Expression Network Analysis to Explore Hub Genes of Resveratrol Biosynthesis in Exocarp and Mesocarp of 'Summer Black' Grape. PLANTS (BASEL, SWITZERLAND) 2023; 12:578. [PMID: 36771662 PMCID: PMC9920568 DOI: 10.3390/plants12030578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Resveratrol is a polyphenol compound beneficial to human health, and its main source is grapes. In the present study, the molecular regulation of resveratrol biosynthesis in developing grape berries was investigated using weighted gene co-expression network analysis (WGCNA). At the same time, the reason for the resveratrol content difference between grape exocarp (skin) and mesocarp (flesh) was explored. Hub genes (CHS, STS, F3'5'H, PAL, HCT) related to resveratrol biosynthesis were screened with Cytoscape software. The expression level of hub genes in the exocarp was significantly higher than that in the mesocarp, and the expressions of the hub genes and the content of resveratrol in exocarp peaked at the maturity stage. While the expression levels of PAL, CHS and STS in the mesocarp, reached the maximum at the maturity stage, and F3'5'H and HCT decreased. These hub genes likely play a key role in resveratrol biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that resveratrol biosynthesis was related to flavonoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis, and stilbene biosynthesis pathways. This study has theoretical significance for exploring genes related to resveratrol biosynthesis in the exocarp and mesocarp of grapes, and provides a theoretical basis for the subsequent function and regulatory mechanism of hub genes.
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Affiliation(s)
- Chengyue Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lifang Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Quan Fan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengfei He
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Congqiao Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaxing Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruyan Huang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiaqi Tang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shehu A. Tadda
- Department of Agronomy, Faculty of Agriculture, Federal University Dutsin-Ma, Dutsin-Ma 821101, Nigeria
| | - Dongliang Qiu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhipeng Qiu
- Lunong Agricultural Technology Co., Ltd., Xiamen 361100, China
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5
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Integrated Analysis of Widely Targeted Metabolomics and Transcriptomics Reveals the Effects of Transcription Factor NOR-like1 on Alkaloids, Phenolic Acids, and Flavonoids in Tomato at Different Ripening Stages. Metabolites 2022; 12:metabo12121296. [PMID: 36557334 PMCID: PMC9853326 DOI: 10.3390/metabo12121296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Tomato is abundant in alkaloids, phenolic acids, and flavonoids; however, the effect of transcription factor NOR-like1 on these metabolites in tomato is unclear. We used a combination of widely targeted metabolomics and transcriptomics to analyze wild-type tomatoes and CR-NOR-like1 tomatoes. A total of 83 alkaloids, 85 phenolic acids, and 96 flavonoids were detected with significant changes. Combined with a KEGG enrichment analysis, we revealed 16 differentially expressed genes (DEGs) in alkaloid-related arginine and proline metabolism, 60 DEGs were identified in the phenolic acid-related phenylpropane biosynthesis, and 30 DEGs were identified in the flavonoid-related biosynthesis pathway. In addition, some highly correlated differential-expression genes with differential metabolites were further identified by correlation analysis. The present research provides a preliminary view of the effects of NOR-like1 transcription factor on alkaloid, phenolic acid, and flavonoid accumulation in tomatoes at different ripening stages based on widely targeted metabolomics and transcriptomics in plants, laying the foundation for extending fruit longevity and shelf life as well as cultivating stress-resistant plants.
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Wang J, Su H, Wu Z, Wang W, Zhou Y, Li M. Integrated Metabolites and Transcriptomics at Different Growth Stages Reveal Polysaccharide and Flavonoid Biosynthesis in Cynomorium songaricum. Int J Mol Sci 2022; 23:ijms231810675. [PMID: 36142587 PMCID: PMC9501575 DOI: 10.3390/ijms231810675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
Cynomorium songaricum is a perennial parasitic herb, and its stem is widely used as a traditional Chinese medicine, which largely relies on bioactive compounds (e.g., polysaccharides, flavonoids, and triterpenes). To date, although the optimum harvest time of stems has been demonstrated at the unearthed stage (namely the early flowering stage, EFS), the accumulation mechanism of polysaccharides and flavonoids during growth stages is still limited. In this study, the physiological characteristics (stem fresh weight, contents of soluble sugar and flavonoids, and antioxidant capacity) at four different growth stages (germination stage (GS), vegetative growth stage (VGS), EFS, and flowering stage (FS)) were determined, transcriptomics were analyzed by illumina sequencing, and expression levels of key genes were validated by qRT-PCR at the GS, VGS, and EFS. The results show that the stem biomass, soluble sugar and total flavonoids contents, and antioxidant capacity peaked at EFS compared with GS, VGS, and FS. A total of 6098 and 13,023 differentially expressed genes (DEGs) were observed at VGS and EFS vs. GS, respectively, with 367 genes co-expressed. Based on their biological functions, 109 genes were directly involved in polysaccharide and flavonoid biosynthesis as well as growth and development. The expression levels of key genes involved in polysaccharides (e.g., GLCs, XTHs and PMEs), flavonoids (e.g., 4CLLs, CYPs and UGTs), growth and development (e.g., AC58, TCPs and AP1), hormones biosynthesis and signaling (e.g., YUC8, AIPT and ACO1), and transcription factors (e.g., MYBs, bHLHs and WRKYs) were in accordance with changes of physiological characteristics. The combinational analysis of metabolites with transcriptomics provides insight into the mechanism of polysaccharide and flavonoid biosynthesis in C. songaricum during growth stages.
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Affiliation(s)
- Jie Wang
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resource, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Hongyan Su
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhibo Wu
- Station of Alxa League Aviation Forest Guard, Alxa 750306, China
| | - Wenshu Wang
- Alxa Forestry and Grassland Research Institute, Alxa 750306, China
| | - Yubi Zhou
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resource, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence: (Y.Z.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (Y.Z.); (M.L.)
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Yin X, Han L, Zheng W, Cai L, Qin M, He Z, Kang J. Global regulatory factor AaLaeA upregulates the production of antitumor substances in the endophytic fungus Alternaria alstroemeria. J Basic Microbiol 2022; 62:1402-1414. [PMID: 36041052 DOI: 10.1002/jobm.202200391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/30/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022]
Abstract
The global regulatory factor LaeA has been shown to be involved in the biosynthesis of secondary metabolites in various fungi. In a previous work, we isolated an endophytic fungus from Artemisia annua, and its extract had a significant inhibitory effect on the A549 cancer cell line. Phylogenetic analysis further identified the strain as Alternaria alstroemeria. Overexpression of AalaeA gene resulted in significantly increased antitumor activity of this strain's extract. The 3-(4, 5- dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay results showed that the inhibition rate of the AalaeAOE29 mutant extract on A549 cancer cells was significantly higher than that of the WT extract, as the IC50 decreased from 195.0 to 107.4 μg/ml, and the total apoptosis rate was enhanced. Overexpression of the AalaeA gene significantly increased the contents of myricetin, geraniol, ergosterol, and 18 other antitumor compounds as determined by metabolomic analysis. Transcriptomic analysis revealed significant changes in 95 genes in the mutant strain, including polyketide synthases, nonribosomal peptide synthases, cytochrome P450s, glycosyltransferases, acetyl-CoA acetyltransferases, and others. These results suggested that AaLaeA mediated the antitumor activity of the metabolites in A. alstroemeria by regulating multiple metabolic pathways.
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Affiliation(s)
- Xuemin Yin
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Long Han
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Wen Zheng
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Lu Cai
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Min Qin
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Zhangjiang He
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
| | - Jichuan Kang
- College of Pharmacy, Guizhou University, Guiyang, The People's Republic of China.,Southwest Biomedical Resources of the Ministry of Education, Guizhou University, Guiyang, The People's Republic of China
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Fang H, Zheng K, Zhang J, Gu X, Zhao Y, Zheng Y, Wang Q. Differences in gene expression and endophytic bacterial diversity in Atractylodes macrocephala Koidz. rhizomes from different growth years. Can J Microbiol 2022; 68:353-366. [PMID: 35080442 DOI: 10.1139/cjm-2021-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atractylodes macrocephala Koidz. (AMK) is widely used owing to its pharmacological activity in traditional Chinese medicine (TCM). Here, we aimed to characterize the differentially expressed genes (DEGs) of one- and three-year growth (OYG and TYG) rhizomes of AMK combined with the endophytic bacterial diversity analysis using high-throughput RNA-sequencing. 114,572 unigenes were annotated in six public databases. 3570 DEGs revealed a clear difference, of which 936 and 2634 genes were up- and down-regulated, respectively. The results of KEGG pathway analysis indicated that DEGs corresponding to the terpenoid synthesis gene were downregulated in TYG rhizomes. 414,424 sequences corresponding to the 16S rRNA gene were divided into 1267 operational taxonomic units (OTUs). Moreover, the diversity of endophytic bacteria changed with species in OYG (773) and TYG (1201) rhizomes at OTU level, and Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. Comparison of species differences among different growth years revealed that some species were significantly different, such as Actinomycetes, Variovorax, Cloacibacterium, etc. Interestingly, the decrease in the function-related metabolism of terpenoids and polyketides was found to be correlated the low expression of terpene synthesis genes in TYG rhizomes assessed using PICRUSt2. These data provide a scientific basis for elucidating the mechanism underlying metabolite accumulation and endophytic bacterial diversity in relation to the growth years in AMK.
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Affiliation(s)
- Huiyong Fang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, College of Pharmacy, China;
| | - Kaiyan Zheng
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Jianyun Zhang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China, 050200.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China, 050200;
| | - Xian Gu
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Yanyun Zhao
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
| | - Yuguang Zheng
- Hebei Chemical and Pharmaceutical College, 118457, Shijiazhuang, Hebei, China.,Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China;
| | - Qian Wang
- Hebei University of Chinese Medicine, 441322, Traditional Chinese Medicine Processing Technology Innovation Center of Hebei Province, Shijiazhuang, China.,Hebei University of Chinese Medicine, 441322, College of Pharmacy, Shijiazhuang, China;
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Sun HF, Song MF, Zhang Y, Zhang ZL. Transcriptome profiling reveals candidate flavonoid-related genes during formation of dragon's blood from Dracaena cochinchinensis (Lour.) S.C.Chen under conditions of wounding stress. JOURNAL OF ETHNOPHARMACOLOGY 2021; 273:113987. [PMID: 33667570 DOI: 10.1016/j.jep.2021.113987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Dragon's Blood (Resina Draconis) is a red resin that has been used in traditional medicine to promote blood circulation, regenerate muscles, reduce swelling and pain, stop bleeding, etc., and its main chemical constituents are flavonoids. Dracaena cochinchinensis (Lour.) S.C.Chen is the only plant defined by the Pharmacopoeia of the People's Republic of China as a source of dragon's blood. AIM OF THE STUDY We aimed to reveal genes involved in the biosynthesis and accumulation of flavonoids of D. cochinchinensis which is under wounding stress by performing a de novo transcriptome analysis. MATERIALS AND METHODS D. cochinchinensis samples were collected for transcriptome sequencing and bioinformatics analysis at 0 days (0 d), 3 days (3 d), 6 days (6 d), and 10 days (10 d) after induction wounding stress, and tissues were microscopically observed after wounding stress. RESULTS A total of 63,244 unigenes were obtained through bioinformatics analysis, and genes associated with the biosynthesis of flavonoids were identified. Through the analysis of DEGs after wounding stress in D. cochinchinensis, based on gene expression consistent with flavonoid accumulation levels, 20 genes in connection with the flavonoid synthesis pathway and 56 genes that may be responsible for flavonoid modification and transport, and also revealed TFs (MYB, bHLH) that may be responsible for flavonoid biosynthesis. Analysis of DEGs between the four periods revealed that after wounding stress, the greatest number of significant DEGs were enriched during the first 3 days, while fewer DEGs were enriched after day 3, which corresponding to only about 1/10 (353/3883) the number of DEGs during the first 3 days. In addition, putative unigenes involved in lignin biosynthesis, such as CSE, HCT, CCR, F5H, and CAD, were significantly down-regulation after D. cochinchinensis wounding stress, but the putative unigenes responsible for flavonoid biosynthesis, such as CHS, CHI, DFR, F3'5'H, F3H, ANR, FLS, and ANS were significantly up-regulation. CONCLUSION We performed de novo transcriptome analysis of D.cochinchinensis under wounding stress, candidate genes and TFs involved in the biosynthesis and accumulation of flavonoids were identified, which is the first report on the transcript variants in flavonoid form accumulation in D. cochinchinensis under wounding stress. According to the results of DEGs analysis, wounding stress attenuated lignin biosynthesis meanwhile promoted flavonoid biosynthesis. In addition, we also compared the transcriptomics of the two different original plants (D.cochinchinensis and D.cambodiana) that form dragon's blood in order to provide further understanding of the formation of dragon's blood.
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Affiliation(s)
- Hui-Fang Sun
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Mei-Fang Song
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Yue Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Zhong-Lian Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China.
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Li P, Ruan Z, Fei Z, Yan J, Tang G. Integrated Transcriptome and Metabolome Analysis Revealed That Flavonoid Biosynthesis May Dominate the Resistance of Zanthoxylum bungeanum against Stem Canker. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6360-6378. [PMID: 34043342 DOI: 10.1021/acs.jafc.1c00357] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Stem canker of Zanthoxylum bungeanum is a devastating disease that seriously affects the plantation and industrial development of Z. bungeanum due to a lack of effective control measures. The objective of this study was to screen out resistant Z. bungeanum varieties and further explore their resistance mechanisms against stem canker. Results showed that the most resistant and susceptible varieties were, respectively, Doujiao (DJ) and Fengxian Dahongpao (FD). Combining transcriptomic and metabolomic analyses, we found that the genes and metabolites associated with the phenylpropanoid metabolism, especially flavonoid biosynthesis, were highly significantly enriched in DJ following pathogen infection compared with that in FD, which indicated that the flavonoid metabolism may positively dominate the resistance of Z. bungeanum. This finding was further confirmed by quantitative real-time polymerase chain reaction analysis, through which higher expression levels of core genes involved in flavonoid metabolism in resistant variety were observed. Moreover, by analyzing the differences in the flavonoid content in the stems of resistant and susceptible varieties and the antifungal activities of flavonoids extracted from Z. bungeanum stems, the conclusion that flavonoid metabolism positively regulates the resistance of Z. bungeanum was further supported. Our results not only aid in better understanding the resistance mechanisms of Z. bungeanum against stem canker but also promote the breeding and utilization of resistant varieties.
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Affiliation(s)
- Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Zhaoxue Fei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jinjiao Yan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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Yuan L, Pan K, Li Y, Yi B, Gao B. Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes. BMC Genom Data 2021; 22:19. [PMID: 34090339 PMCID: PMC8180045 DOI: 10.1186/s12863-021-00973-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. RESULTS In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves. CONCLUSION The DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.
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Affiliation(s)
- Lin Yuan
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Kun Pan
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Yonghui Li
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Bo Yi
- Department of Pharmacy, 928th Hospital of PLA Joint Logistics Support Force, Haikou, 571159, China.
| | - Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China.
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