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Zhao JX, Wang S, Liu J, Jiang XD, Wen J, Suo ZQ, Liu J, Zhong MC, Wang Q, Gu Z, Liu C, Deng Y, Hu JY, Li DZ. A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1842-1855. [PMID: 37665679 DOI: 10.1111/tpj.16452] [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: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full-length transcriptome resource incorporated into the BlueOmics database (http://blueomics.iflora.cn) for two Strobilanthes species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso-seq reads together with ~185 and ~75 Gb strand-specific RNA seq data, we annotated 80 971 and 79 985 non-redundant full-length transcripts for the perennial polycarpic Strobilanthes tetrasperma and the perennial monocarpic Strobilanthes biocullata, respectively. In S. tetrasperma, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in S. tetrasperma and S. biocullata, respectively. Interestingly, among the 33 transcription factors showing differential expression in S. tetrasperma but without differential expression in S. biocullata, three were involved potentially in the photoperiod and circadian-clock pathway of flowering time regulation (FAR1 RELATED SEQUENCE 12, FRS12; NUCLEAR FACTOR Y A1, NFYA1; PSEUDO-RESPONSE REGULATOR 5, PRR5), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.
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Affiliation(s)
- Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jiazhi Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Wen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Quan Suo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhirong Gu
- Administration of National Nature Reserve of Badagongshan, Sangzhi, 427000, Hunan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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Liu C, Cheng M, Ma C, Chen J, Tan H. Identification of novel flavin-dependent monooxygenase from Strobilanthes Cusia reveals molecular basis of indoles' biosynthetic logic. BMC PLANT BIOLOGY 2023; 23:527. [PMID: 37904107 PMCID: PMC10617207 DOI: 10.1186/s12870-023-04557-5] [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: 04/13/2023] [Accepted: 10/23/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Strobilanthes cusia (Nees) Kuntze is a traditional medical plant distributed widely in south China. The indole compounds that originated from the plant are responsible for its pharmacological activities. However, the reason why indole ingredients are accumulated in this herb and how it is biosynthesized has remained largely unknown. RESULTS In this study, metabolic and transcriptional profiling measurement experiments of different S. cusia organs were carried out to understand the underlying molecular basis of indoles' biosynthetic logic. A metabolic investigation demonstrated that the indoles are primarily accumulated mainly in aerial parts, particularly in leaves. RNA-seq was employed to reveal the organ specific accumulation of indoles in different S. cusia organs. Meanwhile, a flavin-dependent monooxygenase gene (ScFMO1) was found in S. cusia, and it has capacity to produce indoxyl from indole by the fermentation assay. Finally, we assessed the outcomes of transient expression experiment in tobacco and confirmed that ScFMO1 localizes in cytoplasm. CONCLUSIONS Our results suggest that ScFMO1 plays a key role in biosynthesis of indoles (Indigo, indirubin, indican, etc.), it will be useful for illuminating the molecular basis of the medicinal indoles' biosynthesis and developing strategies for improving their yields.
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Affiliation(s)
- Chang Liu
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Mengya Cheng
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chao Ma
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Junfeng Chen
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hexin Tan
- Department Chinese Medicine Authentication, College of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, China.
- Department of Pharmacy, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, China.
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Yang B, Zheng M, Dong W, Xu P, Zheng Y, Yang W, Luo Y, Guo J, Niu D, Yu Y, Jiang C. Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment. Microbiol Spectr 2023; 11:e0361122. [PMID: 36786562 PMCID: PMC10100852 DOI: 10.1128/spectrum.03611-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.
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Affiliation(s)
- Bingye Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Mingzi Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Wenpan Dong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Peiling Xu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Wei Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake/Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake/Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Jianhua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Yiyang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Chunhao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
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Guo Z, Chen J, Lv Z, Huang Y, Tan H, Zhang L, Diao Y. Molecular cloning and functional characterization of BcTSA in the biosynthesis of indole alkaloids in Baphicacanthus cusia. FRONTIERS IN PLANT SCIENCE 2023; 14:1174582. [PMID: 37139111 PMCID: PMC10149986 DOI: 10.3389/fpls.2023.1174582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
Baphicacanthus cusia (Nees) Bremek (B. cusia) is an essential traditional Chinese herb that is commonly used to treat colds, fever, and influenza. Indole alkaloids, such as indigo and indirubin, are the primary active constituents of B. cusia. The indole-producing reaction is crucial for regulating the flow of indole alkaloids metabolites along the pathways and coordinating primary and secondary product biosynthesis in plants. The tryptophan synthase alpha-subunit (TSA) can catalyse a process that produces indole, which is free to enter secondary metabolite pathways; however, the underlying potential mechanism of regulating indigo alkaloids synthesis remains unknown. Here, a BcTSA was cloned from the transcriptome of B. cusia. The BcTSA has a significant degree of similarity with other plant TSAs according to bioinformatics and phylogenetic analyses. Quantitative real-time PCR (RT-qPCR) research showed that BcTSA was dramatically enhanced in response to treatment with methyl jasmonate (MeJA), salicylic acid (SA), and abscisic acid (ABA), and was predominantly expressed in the stems as opposed to the leaves and rhizomes. Subcellular localization revealed that BcTSA is localized in chloroplasts, which is compatible with the fact that the conversion of indole-3-glycerol phosphate (IGP) to indole occurs in chloroplasts. The complementation assay results showed that BcTSA was functional, demonstrating that it was capable of catalyzing the conversion of IGP to indole. BcTSA was shown to stimulate the manufacture of indigo alkaloids including isatin, indigo, and indirubin when the gene was overexpressed in the hairy roots of Isatis indigotica. In conclusion, our research provides novel perspectives that might be applied to manipulating the indole alkaloid composition of B. cusia.
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Affiliation(s)
- Zhiying Guo
- School of Food and Bioengineering, Fujian Polytechnic Normal University, Fuqing, China
- School of Medicine, Huaqiao University, Quanzhou, China
| | - Junfeng Chen
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zongyou Lv
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuxiang Huang
- School of Medicine, Huaqiao University, Quanzhou, China
| | - Hexin Tan
- School of Pharmacy, Navy Medical University, Shanghai, China
- *Correspondence: Hexin Tan, ; Lei Zhang, ; Yong Diao,
| | - Lei Zhang
- School of Pharmacy, Navy Medical University, Shanghai, China
- *Correspondence: Hexin Tan, ; Lei Zhang, ; Yong Diao,
| | - Yong Diao
- School of Medicine, Huaqiao University, Quanzhou, China
- *Correspondence: Hexin Tan, ; Lei Zhang, ; Yong Diao,
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5
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Zeng M, Zhong Y, Guo Z, Yang H, Zhu H, Zheng L, Diao Y. Expression and Functional Study of BcWRKY1 in Baphicacanthus cusia (Nees) Bremek. FRONTIERS IN PLANT SCIENCE 2022; 13:919071. [PMID: 35845683 PMCID: PMC9284225 DOI: 10.3389/fpls.2022.919071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Baphicacanthus cusia (Nees) Bremek (B. cusia) is an important medicinal plant. Its effective substances including indigo and indirubin are metabolites in indoleacetate metabolic pathway. Based on a previous transcriptome sequencing analysis, a WRKY transcription factor, BcWRKY1, in B. cusia was identified, showing significant correlation with effective substances from B. cusia. In this study, BcWRKY1 was cloned by reverse transcription-polymerase chain reaction (RT-PCR). Further analysis showed that the BcWRKY1 gene was 916 bp in length, containing three exons and two introns. The open reading frame (ORF) of BcWRKY1 was 534 bp in length and encoded a WRKY domain-containing protein with 177 amino acids residues. Subcellular localization showed that BcWRKY1 protein was mainly localized in the nucleus. It could bind to the W-box motif and its role in transcriptional activation was confirmed in yeast. The function of BcWRKY1 was investigated by overexpressing BcWRKY1 in Arabidopsis thaliana. Metabolic profiles in wild type and BcWRKY1-OX1 transgenic Arabidopsis thaliana were analyzed with LC-MS. Results showed that the metabolic profile was significantly changed in BcWRKY1-OX1 transgenic Arabidopsis thaliana compared with wild type. Furthermore, indole-related metabolites were significantly increased in BcWRKY1-OX1 transgenic Arabidopsis thaliana, and the metabolic pathway analysis showed that flavonoid biosynthesis was significantly enriched. Overexpression of BcWRKY1 significantly changed flavonoid and indole metabolism and indole-related metabolites were significantly upregulated. We postulated that the BcWRKY1 transcription factor might be involved in the regulation of effective substances metabolism in B. cusia.
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Affiliation(s)
- Meijuan Zeng
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiying Guo
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
- Fujian Polytechnic Normal University, Fuqing, China
| | - Huiyong Yang
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
| | - Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liling Zheng
- Department of Cardiovascular Surgery, First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
| | - Yong Diao
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
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Optimization of Extraction of Bioactive Compounds from Baphicacanthus cusia Leaves by Hydrophobic Deep Eutectic Solvents. Molecules 2021; 26:molecules26061729. [PMID: 33808811 PMCID: PMC8003621 DOI: 10.3390/molecules26061729] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Deep eutectic solvents (DESs) are considered as efficient and green solvents for the extraction of bioactive compounds from medicinal plants. In this work, a novel method of DES-based ultrasound-assisted extraction of bioactive compounds from Baphicacanthus cusia leaves (BCL) was established. Systematic screening and the morphology of the original and treated BCL were observed with scanning electron microscopy to determine the extraction efficiency of different solvents. The extraction conditions were optimized by Box–Behnken design (BBD) tests and the optimal extraction conditions were as follows: lactic acid/L-menthol ratio of 5: 2 (mol/mol), solid–liquid ratio of 80.0 mL/g and temperature of 60.5 °C. The extraction yields of tryptanthrin, indigo and indirubin reached 0.356, 1.744 and 0.562 mg/g, respectively. The results of a 2,2-diphenyl-1-picrylhydrazy (DPPH) radical scavenging activity test indicated the feasibility of DESs in the extraction of bioactive compounds. This study indicated that L-menthol/lactic acid was a green and efficient solvent for the extraction of bioactive compounds from BCL, and DES-based ultrasound-assisted extraction could be used as an effective application strategy for the extraction of bioactive compounds from medicinal plants.
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Hu Y, Ma D, Ning S, Ye Q, Zhao X, Ding Q, Liang P, Cai G, Ma X, Qin X, Wei D. High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids. FRONTIERS IN PLANT SCIENCE 2021; 12:742420. [PMID: 34659312 PMCID: PMC8515051 DOI: 10.3389/fpls.2021.742420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/26/2021] [Indexed: 05/21/2023]
Abstract
Strobilanthes cusia (Nees) Kuntze is an important plant used to process the traditional Chinese herbal medicines "Qingdai" and "Nanbanlangen". The key active ingredients are indole alkaloids (IAs) that exert antibacterial, antiviral, and antitumor pharmacological activities and serve as natural dyes. We assembled the S. cusia genome at the chromosome level through combined PacBio circular consensus sequencing (CCS) and Hi-C sequencing data. Hi-C data revealed a draft genome size of 913.74 Mb, with 904.18 Mb contigs anchored into 16 pseudo-chromosomes. Contig N50 and scaffold N50 were 35.59 and 68.44 Mb, respectively. Of the 32,974 predicted protein-coding genes, 96.52% were functionally annotated in public databases. We predicted 675.66 Mb repetitive sequences, 47.08% of sequences were long terminal repeat (LTR) retrotransposons. Moreover, 983 Strobilanthes-specific genes (SSGs) were identified for the first time, accounting for ~2.98% of all protein-coding genes. Further, 245 putative centromeric and 29 putative telomeric fragments were identified. The transcriptome analysis identified 2,975 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and triterpenoid biosynthesis. This systematic characterization of key enzyme-coding genes associated with the IA pathway and basic helix-loop-helix (bHLH) transcription factor family formed a network from the shikimate pathway to the indole alkaloid synthesis pathway in S. cusia. The high-quality S. cusia genome presented herein is an essential resource for the traditional Chinese medicine genomics studies and understanding the genetic underpinning of IA biosynthesis.
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Affiliation(s)
- Yongle Hu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Ecology and Resource Engineering, Wuyi University, Wuyishan, China
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, Wuyishan, China
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shuju Ning
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qi Ye
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanxuan Zhao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiansu Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Pingping Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Guoqian Cai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaomao Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xia Qin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Daozhi Wei
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Daozhi Wei
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Xu W, Zhang L, Cunningham AB, Li S, Zhuang H, Wang Y, Liu A. Blue genome: chromosome-scale genome reveals the evolutionary and molecular basis of indigo biosynthesis in Strobilanthes cusia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:864-879. [PMID: 32981147 DOI: 10.1111/tpj.14992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Natural plant dyes have been developed and used across many traditional societies worldwide. The blue pigment indigo has seen widespread usage across South America, Egypt, Europe, India and China for thousands of years, mainly extracted from indigo-rich plants. The utilization and genetic engineering of indigo in industries and ethnobotanical studies on the effects of cultural selection on plant domestication are limited due to lack of relevant genetic and genomic information of dye plants. Strobilanthes cusia (Acanthaceae) is a typical indigo-rich plant important to diverse ethnic cultures in many regions of Asia. Here we present a chromosome-scale genome for S. cusia with a genome size of approximately 865 Mb. About 79% of the sequences were identified as repetitive sequences and 32 148 protein-coding genes were annotated. Metabolic analysis showed that the main indigoid pigments (indican, indigo and indirubin) were mainly synthesized in the leaves and stems of S. cusia. Transcriptomic analysis revealed that the expression level of genes encoding metabolic enzymes such as monooxygenase, uridine diphosphate-glycosyltransferase and β-glucosidase were significantly changed in leaves and stems compared with root tissues, implying their participation in indigo biosynthesis. We found that several gene families involved in indigo biosynthesis had undergone an expansion in number, with functional differentiation likely facilitating indigo biosynthesis in S. cusia. This study provides insight into the physiological and molecular bases of indigo biosynthesis, as well as providing genomic data that provide the basis for further study of S. cusia cultivation by Asia's traditional textile producers.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Libin Zhang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Anthony B Cunningham
- School of Veterinary and Life Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Shan Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Huifu Zhuang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Yuhua Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
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Qiu X, Xu Y, Xiong B, Dai L, Huang S, Dong T, Sun G, Liao L, Deng Q, Wang X, Zhu J, Wang Z. Effects of exogenous methyl jasmonate on the synthesis of endogenous jasmonates and the regulation of photosynthesis in citrus. PHYSIOLOGIA PLANTARUM 2020; 170:398-414. [PMID: 32691420 DOI: 10.1111/ppl.13170] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/28/2020] [Accepted: 07/15/2020] [Indexed: 05/21/2023]
Abstract
Methyl jasmonate (MeJA) is an airborne signaling phytohormone that can induce changes in endogenous jasmonates (JAs) and cause photosynthetic responses. However, the response of these two aspects of citrus plants at different MeJA concentrations is still unclear. Four MeJA concentrations were used in two citrus varieties, Huangguogan (C. reticulata × C. sinensis) and Shiranuhi [C. reticulata × (C. reticulata × C. sinensis)], to investigate the effects of MeJA dose on the endogenous JAs pathway and photosynthetic capacity. We observed that MeJA acted in a dose-dependent manner, and its stimulation in citrus leaves showed a bidirectional character at different concentrations. This work demonstrates that MeJA at only a concentration of 2.2 mM or less contributed to the activation of magnesium protoporphyrin IX methyltransferase (ChlM, EC 2.1.1.11) and protochlorophyllide oxidoreductase (POR, EC 1.3.1.11) and the simultaneous accumulation of Chl a and Chl b, which in turn contributed to an improved photosynthetic capacity and PSII photochemistry efficiency of citrus. Meanwhile, the inhibition of endogenous JAs synthesis by exogenous MeJA was observed. This was achieved by reducing the ratio of monogalactosyl diacylglycerol (MGDG) to diagalactosyl diacylglycerol (DGDG) and inhibiting the activities of key enzymes in JAs synthesis, especially 12-oxo-phytodienoic acid reductase (OPR, EC 1.3.1.42). Another noteworthy finding is that there may exist a JA-independent pathway that could regulate 12-oxo-phytodienoic acid (OPDA) synthesis. This study jointly analyzed the internal hormone regulation mechanism and the external physiological response, as well as revealed the effects of exogenous MeJA on promoting the photosynthesis and inhibiting the endogenous JAs synthesis.
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Affiliation(s)
- Xia Qiu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghuan Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Neusoft Institute Guangdong, Guangdong, 528225, China
| | - Bo Xiong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lin Dai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shengjia Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tiantian Dong
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guochao Sun
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling Liao
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qunxian Deng
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xun Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jin Zhu
- Sichuan Horticultural Crop Extension Station, Sichuan, 610041, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130, China
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