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Hu X, Zhu T, Min X, He J, Hou C, Liu X. Integrated Metabolomic and Transcriptomic Analysis of Puerarin Biosynthesis in Pueraria montana var. thomsonii at Different Growth Stages. Genes (Basel) 2023; 14:2230. [PMID: 38137052 PMCID: PMC10742406 DOI: 10.3390/genes14122230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Puerarin, a class of isoflavonoid compounds concentrated in the roots of Puerarias, has antipyretic, sedative, and coronary blood-flow-increasing properties. Although the biosynthetic pathways of puerarin have been investigated by previous researchers, studies focusing on the influence of different growth stages on the accumulation of metabolites in the puerarin pathway are not detailed, and it is still controversial at the last step of the 8-C-glycosylation reaction. In this study, we conducted a comprehensive analysis of the metabolomic and transcriptomic changes in Pueraria montana var. thomsonii during two growing years, focusing on the vigorous growth and dormant stages, to elucidate the underlying mechanisms governing the changes in metabolite and gene expression within the puerarin biosynthesis pathway. In a comparison of the two growth stages in the two groups, puerarin and daidzin, the main downstream metabolites in the puerarin biosynthesis pathway, were found to accumulate mainly during the vigorous growth stage. We also identified 67 common differentially expressed genes in this pathway based on gene expression differences at different growth stages. Furthermore, we identified four candidate 8-C-GT genes that potentially contribute to the conversion of daidzein into puerarin and eight candidate 7-O-GT genes that may be involved in the conversion of daidzein into daidzin. A co-expression network analysis of important UGTs and HIDs along with daidzein and puerarin was conducted. Overall, our study contributes to the knowledge of puerarin biosynthesis and offers information about the stage at which the 8-C-glycosylation reaction occurs in biosynthesis. These findings provide valuable insights into the cultivation and quality enhancement of Pueraria montana var. thomsonii.
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Affiliation(s)
| | | | | | | | | | - Xia Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan 430070, China; (X.H.); (T.Z.); (X.M.); (J.H.); (C.H.)
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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Xufeng X, Yuanfeng H, Ming Z, Shucheng S, Haonan Z, Weifeng Z, Fei G, Caijun W, Shuying F. Transcriptome profiling reveals the genes involved in tuberous root expansion in Pueraria (Pueraria montana var. thomsonii). BMC PLANT BIOLOGY 2023; 23:338. [PMID: 37365513 DOI: 10.1186/s12870-023-04303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/20/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Pueraria is a dry root commonly used in Traditional Chinese Medicine or as food and fodder, and tuberous root expansion is an important agronomic characteristic that influences its yield. However, no specific genes regulating tuberous root expansion in Pueraria have been identified. Therefore, we aimed to explore the expansion mechanism of Pueraria at six developmental stages (P1-P6), by profiling the tuberous roots of an annual local variety "Gange No.1" harvested at 105, 135, 165, 195, 225, and 255 days after transplanting. RESULTS Observations of the tuberous root phenotype and cell microstructural morphology revealed that the P3 stage was a critical boundary point in the expansion process, which was preceded by a thickening diameter and yield gain rapidly of the tuberous roots, and followed by longitudinal elongation at both ends. A total of 17,441 differentially expressed genes (DEGs) were identified by comparing the P1 stage (unexpanded) against the P2-P6 stages (expanded) using transcriptome sequencing; 386 differential genes were shared across the six developmental stages. KEGG pathway enrichment analysis showed that the DEGs shared by P1 and P2-P6 stages were mainly involved in pathways related to the "cell wall and cell cycle", "plant hormone signal transduction", "sucrose and starch metabolism", and "transcription factor (TF)". The finding is consistent with the physiological data collected on changes in sugar, starch, and hormone contents. In addition, TFs including bHLHs, AP2s, ERFs, MYBs, WRKYs, and bZIPs were involved in cell differentiation, division, and expansion, which may relate to tuberous root expansion. The combination of KEGG and trend analyses revealed six essential candidate genes involved in tuberous root expansion; of them, CDC48, ARF, and EXP genes were significantly upregulated during tuberous root expansion while INV, EXT, and XTH genes were significantly downregulated. CONCLUSION Our findings provide new insights into the complex mechanisms of tuberous root expansion in Pueraria and candidate target genes, which can aid in increasing Pueraria yield.
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Affiliation(s)
- Xiao Xufeng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hu Yuanfeng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhang Ming
- Department of Biological Engineering, Jiangxi Biotech Vocational College, Nanchang, 330200, China
| | - Si Shucheng
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Haonan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhu Weifeng
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Ge Fei
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Wu Caijun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Fan Shuying
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
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Wu Z, Zeng W, Li C, Wang J, Shang X, Xiao L, Cao S, Zhang Y, Xu S, Yan H. Genome-wide identification and expression pattern analysis of R2R3-MYB transcription factor gene family involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii. BMC PLANT BIOLOGY 2023; 23:107. [PMID: 36814206 PMCID: PMC9945399 DOI: 10.1186/s12870-023-04115-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND R2R3-MYB transcription factors regulate secondary metabolism, stress responses and development in various plants. Puerarin is a bioactive ingredient and most abundant secondary metabolite isolated from Pueraria lobata. The biosynthesis of puerarin proceeds via the phenylpropanoid pathway and isoflavonoids pathway, in which 9 key enzymes are involved. The expression of these structural genes is under control of specific PtR2R3-MYB genes in different plant tissues. However, how PtR2R3-MYB genes regulates structural genes in puerarin biosynthesis remains elusive. This study mined the PtR2R3-MYB genes involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii. RESULTS A total of 209 PtR2R3-MYB proteins were identified, in which classified into 34 subgroups based on the phylogenetic topology and the classification of the R2R3-MYB superfamily in Arabidopsis thaliana. Furtherly physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze PtR2R3-MYBs. Combining puerarin content and RNA-seq data, speculated on the regulated puerarin biosynthesis of PtR2R3-MYB genes and structural genes, thus 21 PtR2R3-MYB genes and 25 structural genes were selected for validation gene expression and further explore its response to MeJA and GSH treatment by using qRT-PCR analysis technique. Correlation analysis and cis-acting element analysis revealed that 6 PtR2R3-MYB genes (PtMYB039, PtMYB057, PtMYB080, PtMYB109, PtMYB115 and PtMYB138) and 7 structural genes (PtHID2, PtHID9, PtIFS3, PtUGT069, PtUGT188, PtUGT286 and PtUGT297) were directly or indirectly regulation of puerarin biosynthesis in ZG11. It is worth noting that after MeJA and GSH treatment for 12-24 h, the expression changes of most candidate genes were consistent with the correlation of puerarin biosynthesis, which also shows that MeJA and GSH have the potential to mediate puerarin biosynthesis by regulating gene expression in ZG11. CONCLUSIONS Overall, this study provides a comprehensive understanding of the PtR2R3-MYB and will paves the way to reveal the transcriptional regulation of puerarin biosynthesis and response to phytohormone of PtR2R3-MYB genes in Pueraria lobata var. thomsonii.
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Affiliation(s)
- Zhengdan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Changfu Li
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yansheng Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou, 510640, China
| | - Huabing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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Hou L, Wang M, Zhu L, Ning M, Bi J, Du J, Kong X, Gu W, Meng Q. Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir. Front Cell Infect Microbiol 2022; 12:997574. [PMID: 36530442 PMCID: PMC9754153 DOI: 10.3389/fcimb.2022.997574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.
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Affiliation(s)
- Libo Hou
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Mengdi Wang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Lei Zhu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Mingxiao Ning
- Institution of Quality Standard and Testing Technology for Agro-product, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Jingxiu Bi
- Institution of Quality Standard and Testing Technology for Agro-product, Shandong Academy of Agricultural Science, Jinan, Shandong, China
| | - Jie Du
- Animal Husbandry and Veterinary College, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, China
| | - Xianghui Kong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu, China,*Correspondence: Qingguo Meng,
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Cheng H, Huang X, Wu S, Wang S, Rao S, Li L, Cheng S, Li L. Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi. Biomolecules 2022; 12:biom12121731. [PMID: 36551157 PMCID: PMC9775041 DOI: 10.3390/biom12121731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Pueraria lobata (wild.) Ohwi is a leguminous plant and one of the traditional Chinese herbal medicines. Its puerarin extract is widely used in the pharmaceutical industry. This study reported a chromosome-level genome assembly for P. lobata and its characteristics. The genome size was ~939.2 Mb, with a contig N50 of 29.51 Mbp. Approximately 97.82% of the assembled sequences were represented by 11 pseudochromosomes. We identified that the repetitive sequences accounted for 63.50% of the P. lobata genome. A total of 33,171 coding genes were predicted, of which 97.34% could predict the function. Compared with other species, P. lobata had 757 species-specific gene families, including 1874 genes. The genome evolution analysis revealed that P. lobata was most closely related to Glycine max and underwent two whole-genome duplication (WGD) events. One was in a gamma event shared by the core dicotyledons at around 65 million years ago, and another was in the common ancestor shared by legume species at around 25 million years ago. The collinearity analysis showed that 61.45% of the genes (54,579 gene pairs) in G. max and P. lobata had collinearity. In this study, six unique PlUGT43 homologous genes were retrieved from the genome of P. lobata, and no 2-hydroxyisoflavanone 8-C-glucoside was found in the metabolites. This also revealed that the puerarin synthesis was mainly from the glycation of daidzein. The combined transcriptome and metabolome analysis suggested that two bHLHs, six MYBs and four WRKYs were involved in the expression regulation of puerarin synthesis structural genes. The genetic information obtained in this study provided novel insights into the biological evolution of P. lobata and leguminous species, and it laid the foundation for further exploring the regulatory mechanism of puerarin synthesis.
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Affiliation(s)
- Hua Cheng
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China
| | - Xiaohua Huang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China
| | - Shuai Wu
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shiyan Wang
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
| | - Li Li
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
| | - Linling Li
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan 430023, China
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China
- Correspondence: ; Tel.: +86-173-7156-9920
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Niu YF, Li GH, Zheng C, Liu ZY, Liu J. Insights to the superoxide dismutase genes and its roles in Hevea brasiliensis under abiotic stress. 3 Biotech 2022; 12:274. [PMID: 36110566 PMCID: PMC9468202 DOI: 10.1007/s13205-022-03328-7] [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: 12/15/2021] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
The superoxide dismutase (SOD) protein significantly influences the development and growth of plants and their reaction to abiotic stresses. However, little is known about the characteristics of rubber tree SOD genes and their expression changes under abiotic stresses. The present study recognized 11 SOD genes in the rubber tree genome, including 7 Cu/ZnSODs, 2 MnSODs, and 2 FeSODs. Except for HbFSD1, SODs were scattered on five chromosomes. The phylogenetic analysis of SOD proteins in rubber trees and a few other plants demonstrated that the SOD proteins contained three major subgroups. Moreover, the genes belonging to the same clade contained similar gene structures, which confirmed their classification further. The extension of the SOD gene family in the rubber tree was mainly induced by the segmental duplication events. The cis-acting components analysis showed that HbSODs were utilized in many biological procedures. The transcriptomics data indicated that the phosphorylation of the C-terminal domain of RNA polymerase II might control the cold response genes through the CBF pathway and activate the SOD system to respond to cold stress. The qRT-PCR results showed that the expression of HbCSD1 was significantly downregulated under drought and salt stresses, which might dominate the adaption capability to different stresses. Additionally, salt promoted the expression levels of HbMSD1 and HbMSD2, exhibiting their indispensable role in the salinity reaction. The study results will provide a theoretical basis for deep research on HbSODs in rubber trees. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03328-7.
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Affiliation(s)
- Ying-Feng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Guo-Hua Li
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Cheng Zheng
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Zi-Yan Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, 666100 China
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Liu C, Pan J, Yin ZG, Feng T, Zhao J, Dong X, Zhou Y. Integrated transcriptome and metabolome analyses revealed regulatory mechanisms of flavonoid biosynthesis in Radix Ardisia. PeerJ 2022; 10:e13670. [PMID: 35789656 PMCID: PMC9250311 DOI: 10.7717/peerj.13670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/10/2022] [Indexed: 01/17/2023] Open
Abstract
Background Radix Ardisia (Jab Bik Lik Jib) is a common Miao medicine and is widely distributed in the Guizhou region of southern China. The botanical origin of Radix Ardisia includes the dry root and rhizome of Ardisia Crenata Sims (ACS) or Ardisia Crispa (Thunb.) A.DC. (AC), which are closely related species morphologically. However, the secondary metabolites in their roots are different from one another, especially the flavonoids, and these differences have not been thoroughly explored at the molecular level. This project preliminarily identified regulatory molecular mechanisms in the biosynthetic pathways of the flavonoids between ACS and AC using a multi-omics association analysis. Methods In this study, we determined the total levels of saponin, flavonoid, and phenolic in Radix Ardisia from different origins. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially expressed metabolites (DEM). We also performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways, and explore the regulation of flavonoid biosynthesis. Results The total flavonoid and phenolic levels in ACS were significantly higher than in AC (P < 0.05). There were 17,685 DEGs between ACS vs. AC, 8,854 were upregulated and 8,831 were downregulated. Based on this, we continued to study the gene changes in the flavonoid biosynthesis pathway, and 100 DEGs involving flavonoid biosynthesis were differentially expressed in ACS and AC. We validated the accuracy of the RNA-seq data using qRT-PCR. Metabolomic analyses showed that 11 metabolites were involved in flavonoid biosynthesis including: Naringenin, Luteolin, Catechin, and Quercetin. A conjoint analysis of the genome-wide connection network revealed the differences in the types and levels of flavonoid compounds between ACS and AC. The correlation analysis showed that Naringenin, Luteolin, Catechin, and Quercetin were more likely to be key compounds in the flavonoid biosynthesis pathway also including 4CL, AOMT, CHS, CHI, DFR, F3'5'H, FLS, and LAR. Conclusions This study provides useful information for revealing the regulation of flavonoid biosynthesis and the regulatory relationship between metabolites and genes in the flavonoid biosynthesis pathway in Radix Ardisia from different origins.
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Affiliation(s)
- Chang Liu
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jie Pan
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhi-Gang Yin
- Guizhou Engineering Center for Innovative Traditional Chinese Medicine and Ethnic Medicine, Guizhou University, Guiyang, China
| | - Tingting Feng
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jiehong Zhao
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Xiu Dong
- Guizhou Sanli Pharmaceutical Co., Ltd., Guiyang, China
| | - Ying Zhou
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China,Guizhou Engineering Center for Innovative Traditional Chinese Medicine and Ethnic Medicine, Guizhou University, Guiyang, China
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Li Y, Saravana Kumar P, Liu Y, Qiu J, Ran Y, Yuan M, Fang X, Tan X, Zhao R, zhu J, He M. Tailoring enhanced production and identification of isoflavones in the callus cultures of Pueraria thomsonii Benth and its model verification using response surface methodology (RSM): a combined in vitro and statistical optimization. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Scientifically, isoflavones from Pueraria thomsonii Benth possess diverse pharmacological activities and have been used to treat various diseases. In vitro propagation of callus has contributed to the reliability for large-scale production of target compounds. However, the factors affecting the biosynthesis of major isoflavones daidzin, puerarin and daidzein in the callus culture of P. thomsonii are still not known. Therefore, we aimed to enhance the in vitro production of daidzin, puerarin and daidzein by optimizing three independent factors such as temperature, NAA and 6-BA concentrations.
Results
Our findings showed that the optimal concentrations for in vitro biomass production and efficient synthesis of puerarin, daidzin and daidzein were found to be 0.158%, 0.463% and 0.057%, respectively. In addition, the HPLC fingerprint with chemo-metrics analysis was constructed by linear regression of the puerarin, daidzin and daidzein which was found to be in the range of 1.0–36.0, 5.0–72.0 and 1.0–15.0 mg/mL and the LODs and LOQs were found to be 0.15, 0.52, 0.35 and 0.28, 1.50, 0.50 mg/mL for puerarin, daidzin and daidzein, respectively. Surprisingly, our results were also in agreement with the concentration obtained from the model verification for optimal and efficient production of puerarin, daidzin and daidzein which was found to be 0.162%, 0.458% and 0.049%, respectively.
Conclusions
In summary, our present investigation provides new insights that could facilitate the enhanced production of valuable isoflavones in P. thomsonii using plant cell cultures treated with appropriate elicitor combinations and temperature. As far as the authors are concerned, this is the first report on production of daidzin, puerarin and daidzein at higher yield at laboratory level for a wide range of applications in future food, medicinal and pharmaceutical companies.
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10
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Yang S, Zhang X, Zhang X, Bi Y, Gao W. A bZIP transcription factor, PqbZIP1, is involved in the plant defense response of American ginseng. PeerJ 2022; 10:e12939. [PMID: 35282281 PMCID: PMC8916028 DOI: 10.7717/peerj.12939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
American ginseng (Panax quinquefolius L.) is a perennial medicinal plant that has a long usage history in China. However, root rot, which is mainly caused by Fusarium solani can severely reduce the yield and quality of American ginseng, but no disease-resistant variety of American ginseng exists, and the resistance against this disease is not yet well understood. Thus, it is very urgent to analyze the interaction mechanism regulating the interactions between American ginseng and F. solani to mine disease resistance genes. Using transcriptome data and quantitative polymerase chain reaction (qPCR), we screened the transcription factor PqbZIP1 in response to induction by chitin. Yeast self-activation and subcellular localization experiments proved that PqbZIP1 showed transcriptional activity and was localized in the plant nucleus. In addition, qPCR showed that the highest relative expression level was in the roots, wherein chitin and F. solani inhibited and activated the expression of PqbZIP1, respectively, in American ginseng. Additionally, PqbZIP1 significantly inhibited the growth of the Pseudomonas syringae pv. tomato D36E strain in Nicotiana benthamiana, where expressing PqbZIP1 in N. benthamiana increased the jasmonic acid, salicylic acid, and abscisic acid content. Furthermore, PqbZIP1 expression was continually increased upon inoculation with F. solani. Hence, this study revealed that the PqbZIP1 transcription factor might mediate multiple hormonal signaling pathway to modulate root rot disease resistance in American ginseng, and provided important information to breed disease-resistant American ginseng.
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Affiliation(s)
- Shanshan Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,College of Agriculture, Guangxi University, Nanning, China
| | - Xiaoxiao Zhang
- College of Agriculture, Guangxi University, Nanning, China,Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ximei Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanmeng Bi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin, China
| | - Weiwei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Adolfo LM, Rao X, Dixon RA. Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics. BMC PLANT BIOLOGY 2022; 22:10. [PMID: 34979934 PMCID: PMC8722073 DOI: 10.1186/s12870-021-03383-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature. RESULTS We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity. CONCLUSIONS The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.
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Affiliation(s)
- Laci M Adolfo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5017, USA
| | - Xiaolan Rao
- College of Life Sciences, Hubei University, Wuhan, 430068, Hubei Province, China
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5017, USA.
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12
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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13
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Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
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Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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14
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Wang C, Xu N, Cui S. Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis. PeerJ 2021; 9:e10885. [PMID: 33665027 PMCID: PMC7906042 DOI: 10.7717/peerj.10885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. METHODS To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. RESULTS We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.
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Affiliation(s)
- Chenkai Wang
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
- Anhui University, Hefei, China
- Anhui University of Chinese Medicine, Hefei, China
| | - Nenggui Xu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuai Cui
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
- Anhui University of Chinese Medicine, Hefei, China
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15
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Šamec D, Karalija E, Šola I, Vujčić Bok V, Salopek-Sondi B. The Role of Polyphenols in Abiotic Stress Response: The Influence of Molecular Structure. PLANTS (BASEL, SWITZERLAND) 2021; 10:118. [PMID: 33430128 PMCID: PMC7827553 DOI: 10.3390/plants10010118] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 01/15/2023]
Abstract
Abiotic stressors such as extreme temperatures, drought, flood, light, salt, and heavy metals alter biological diversity and crop production worldwide. Therefore, it is important to know the mechanisms by which plants cope with stress conditions. Polyphenols, which are the largest group of plant-specialized metabolites, are generally recognized as molecules involved in stress protection in plants. This diverse group of metabolites contains various structures, from simple forms consisting of one aromatic ring to more complex ones consisting of large number of polymerized molecules. Consequently, all these molecules, depending on their structure, may show different roles in plant growth, development, and stress protection. In the present review, we aimed to summarize data on how different polyphenol structures influence their biological activity and their roles in abiotic stress responses. We focused our review on phenolic acids, flavonoids, stilbenoids, and lignans.
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Affiliation(s)
- Dunja Šamec
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia;
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Zmaja od Bosne 33–35, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Ivana Šola
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.Š.); (V.V.B.)
| | - Valerija Vujčić Bok
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.Š.); (V.V.B.)
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Li Y, He M, Li J, Yao Y, Zhu L, Wu B. Regulatory protein genes and microRNAs in response to selenium stimuli in Pueraria lobata (Willd.) Ohwi. Metallomics 2020; 13:6029134. [PMID: 33570136 DOI: 10.1093/mtomcs/mfaa004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/30/2020] [Accepted: 12/07/2020] [Indexed: 01/28/2023]
Abstract
Regulatory protein genes and microRNAs (miRNAs) play important roles in response to abiotic and biotic stress, and the biosynthesis of secondary metabolites in plants. However, their responses to selenium (Se) stimuli have not been comprehensively studied in Pueraria lobata (Willd.) Ohwi, a selenocompound-rich medicinal and edible plant. In this study, we identified a total of 436/556/1161/624 transcription factors, 134/157/308/172 transcriptional regulators, and 341/456/250/518 protein kinases, which were co-expressed with at least one selenocompound-related structural gene/sulfate transporter or phosphate transporter/reactive oxygen species (ROS) scavenging structural gene/isoflavone-related structural gene, respectively. Then, we identified a total of 87 expressed miRNAs by Se disposure, in which 11 miRNAs, including miR171f-3p, miR390b-3P, miR-N111b, miR-N118, miR-N30, miR-N38-3P, miR-N61a, miR-N61b, miR-N80-3p, miR-N84-3P, and miR-N90.2-3P, were significantly upregulated. We also identified a total of 1172 target genes for the 87 expressed miRNAs. Gene Ontology enrichment analysis of these target genes showed that regulation of transcription, DNA-templated, integral component of membrane, nucleus, ATP binding, and plasma membrane are the top five subclassifications. Finally, we revealed that 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one selenocompound-related structural gene or transporter gene; 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one ROS scavenging structural gene; and 5 miRNAs targeted 9 regulatory protein genes, which are potentially involved in the isoflavone biosynthesis. Overall, the study provides us the comprehensive insight into the roles of regulatory proteins and miRNAs in response to Se stimuli in P. lobata.
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Affiliation(s)
- Yanni Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Meijun He
- Institute of Chinese Medicinal Materials, Hubei Academy of Agricultural Sciences, Enshi 445000, China
| | - Jishuang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yiwei Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
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17
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Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch. Int J Mol Sci 2020; 21:ijms21093101. [PMID: 32353999 PMCID: PMC7247157 DOI: 10.3390/ijms21093101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 01/24/2023] Open
Abstract
Licorice (Glycyrrhiza) is a staple Chinese herbal medicine in which the primary bioactive compound is glycyrrhizic acid (GA), which has important pharmacological functions. To date, the structural genes involved in GA biosynthesis have been identified. However, the regulation of these genes in G. uralensis has not been elucidated. In this study, we performed a comprehensive analysis based on the transcriptome and small RNAome by high-throughput sequencing. In total, we identified 18 structural GA genes and 3924 transporter genes. We identified genes encoding 2374 transporters, 1040 transcription factors (TFs), 262 transcriptional regulators (TRs) and 689 protein kinases (PKs), which were coexpressed with at least one structural gene. We also identified 50,970 alternative splicing (AS) events, in which 17 structural genes exhibited AS. Finally, we also determined that miRNAs potentially targeted 4 structural genes, and 318, 8, and 218 miRNAs potentially regulated 150 TFs, 34 TRs, and 88 PKs, respectively, related to GA. Overall, the results of this study helped to elucidate the gene expression and regulation of GA biosynthesis in G. uralensis, provided a theoretical basis for the synthesis of GA via synthetic biology, and laid a foundation for the cultivation of new varieties of licorice with high GA content.
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18
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Guo K, Yao Y, Yang M, Li Y, Wu B, Lin X. Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi. PeerJ 2020; 8:e8768. [PMID: 32231880 PMCID: PMC7100600 DOI: 10.7717/peerj.8768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/18/2020] [Indexed: 01/04/2023] Open
Abstract
Pueraria lobata (willd.) Ohwi is a consumable selenium-enriched plant used for medicinal purposes. The molecular response to selenium (Se) stimuli in P. lobata is currently unknown. We used RNA-Seq to identify potential genes involved in selenite metabolism and analyzed their expression profiles. We obtained a total of 150,567 unigenes, of which 90,961 were annotated, including 16 structural genes, 14 sulfate transporters, and 13 phosphate transporters that may be involved in Se metabolism, and 33 candidate structural genes involved in isoflavone biosynthesis. The genes with a —foldchange— >2 and q value <0.05 after sodium selenite treatment were identified as differentially expressed genes (DEGs). We obtained a total of 4,246 DEGs, which were enriched in GO terms that included “response to stimulus”, “response to stress”, “signal transduction”, “response to abiotic stimulus”, and “response to chemical”. Of the 4,246 DEGs, one sulfate transporter and five phosphate transporter genes involved Se metabolism, and nine structural genes involved in isoflavone biosynthesis were up-regulated. The expression patterns of 10 DEGs were selected randomly and validated using qRT-PCR. The Pearson Correlation Coefficient (r) was 0.86, indicating the reliability of RNA-Seq results. 22 Reactive Oxygen Species (ROS) scavenging DEGs were found, 11 of which were up-regulated. 436, 624 transcription factors (TFs) correlated with structural genes were identified that may be involved in Se and isoflavone biosynthesis, respectively, using r (r > 0.7 or r < − 0.7). 556 TFs were related to at least one sulfate and phosphate transporter. Our results provided a comprehensive description of gene expression and regulation in response to Se stimuli in P. lobata.
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Affiliation(s)
- Kunyuan Guo
- Institute of Chinese Medicinal Materials, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Yiwei Yao
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Plant Development, beijing, China
| | - Meng Yang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Plant Development, beijing, China
| | - Yanni Li
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Plant Development, beijing, China
| | - Bin Wu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Plant Development, beijing, China
| | - Xianming Lin
- Institute of Chinese Medicinal Materials, Hubei Academy of Agricultural Sciences, Enshi, China
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