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Wang M, Wang Q, Wang X, Wang D, Yin X, Qiao Y, Ma M, Du Y, Wang B. Exploring the potential of Paris polyphylla var. yunnanensis pollen manipulation in modifying seed dormancy. FRONTIERS IN PLANT SCIENCE 2024; 15:1389357. [PMID: 38841278 PMCID: PMC11152045 DOI: 10.3389/fpls.2024.1389357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/16/2024] [Indexed: 06/07/2024]
Abstract
Paris polyphylla var. yunnanensis, a well-known Chinese medicinal herb, shows a unique physiological trait characterized by the cyclic opening and closing of its anthers after pollen maturation. The aim of this study was to explore the implications of this phenomenon on breeding. RNA sequencing coupled with methylation sequencing was used to scrutinize and compare gene expression profiles and methylation alterations in pollen and seeds during anther opening and closing, along with cold exposure. Genes enriched within Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify gene clusters susceptible to temperature-related methylation changes in both pollen and seeds. Four pollen treatment models, namely, normal control, "pollen protected from low temperatures," "pollen from just-opened anther," and "pollen from close-blocked anther," were used to produce corresponding seeds via artificial pollination. Subsequently, qRT-PCR was used to validate modifications in the expression patterns of marker genes in pollinated seeds under diverse treatment scenarios. Genes exhibiting significant differences in expression between anthers and normal tissues, along with gene regions linked to methylation variations attributed to low-temperature-treated pollen and seeds, were identified through transcriptomic analysis. Convergence was observed in three signaling pathways: oxidative phosphorylation (ko00190), plant hormone signal transduction (Ko04075), and zeatin biosynthesis (ko00908). Notably, gene clusters prone to temperature-induced methylation changes, such as NADH-ubiquinone oxidoreductase chain 5, plasma membrane ATPase 4, cytochrome c oxidase subunit 2, cis-zeatin O-glucosyltransferase, ABSCISIC ACID-INSENSITIVE 5-like protein 4, and indole-3-acetic acid-amido synthetase (IAAS), were identified. Evaluation using various pollen pollination models revealed altered expression patterns of five dormancy-regulating marker genes: IAAS, sucrose synthase (SUS), gibberellin 2-oxidase (GA2ox), ABA INSENSITIVE 2 (ABI2), and auxin-repressed protein (ARP), in seeds pollinated with pollen from close-blocked anthers, cold-protected pollen, and pollen from freshly opened anthers. The close-blocked anther treatment led to significantly upregulated expression of IAAS, SUS, GA2ox, and ABI2, whereas ARP expression decreased markedly, indicating a propensity toward prolonged seed dormancy. Conversely, in the low-temperature-protected anther model, SUS, ARP, GA2ox, and IAAS exhibited reduced expression levels, whereas the expression of ABI2 was upregulated, overall facilitating seed germination.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bin Wang
- School of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, China
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Wang D, Huang Y, Rui L, Du H, Qi J, Ma M, Zhou N. Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments. Genes (Basel) 2023; 14:1754. [PMID: 37761894 PMCID: PMC10530812 DOI: 10.3390/genes14091754] [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: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Genetic structure and genetic differentiation were explored using haplotype distribution maps and genetic distance matrices. A total of 15 haplotypes were identified in the 32 populations of P. polyphylla var. yunnanensis. Five unique haplotypes were identified from the fourteen haplotypes of the cultivated populations, while only one unique haplotype was identified from the ten haplotypes of the wild populations. The haplotype richness and genetic diversity of the cultivated populations were higher than those of the wild populations (HT = 0.900 vs. 0.861). In addition, there were no statistically significant correlations between geographic distance and genetic distance in the cultivated populations (r = 0.16, p > 0.05), whereas there was a significant correlation between geographical distance and genetic structure in the wild populations (r = 0.32, p > 0.05), indicating that there was a geographical and genetic connection between the wild populations. There was only 2.5% genetic variation between the wild populations and cultivated populations, indicating no obvious genetic differentiation between the wild and cultivated populations. Overall, the genetic background of the cultivated populations was complex, and it was hypothesized that the unique haplotypes and higher diversity of the cultivated populations were caused by the mixed provenance of the cultivated populations.
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Affiliation(s)
- Dan Wang
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Yu Huang
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
- College of Pharmacy, Dali University, Dali 671000, China
| | - Lu Rui
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Huihui Du
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Junsheng Qi
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
| | - Mingguo Ma
- Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nong Zhou
- The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China; (D.W.); (Y.H.); (L.R.); (H.D.); (J.Q.)
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Wu P, Wang X, Guo J, Zhang S, Li Q, Zhang M, Fang Q, Luo B, Wang H, He W. Analysis of the difference between early-bolting and non-bolting roots of Angelica dahurica based on transcriptome sequencing. Sci Rep 2023; 13:7847. [PMID: 37188680 DOI: 10.1038/s41598-023-34554-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Angelica dahurica (Fisch. ex Hoffm.) Benth.et Hook.f.var.formosana (Boiss.) Shan et Yuan (A. dahurica) is a well-known medicinal plant that has a wide range of applications in the pharmaceutical, food, cosmetic, and other industries. However, the issue of early bolting has emerged as a major hindrance to its production. This problem not only reduces the yield of A. dahurica, but also has an impact on its active ingredients. To date, the molecular factors that contribute to early bolting and its impact on the growth of A. dahurica have not been thoroughly investigated. Therefore, we conducted a transcriptome study using the Illumina NovaSeq 6000 on two developmental types: early-bolting and non-bolting (normal) roots of A. dahurica. We obtained 2,185 up-regulated and 1,414 down-regulated genes in total. Many of the identified transcripts were related to genes involved in early bolting. The gene ontology analysis revealed several differentially expressed genes that are crucial in various pathways, primarily associated with cellular, molecular, and biological processes. Additionally, the morphological characteristics and coumarin content in the early bolting roots of A. dahurica were significantly altered. This study provides insight into the transcriptomic regulation of early bolting in A. dahurica, which can potentially be utilized to enhance its medicinal properties.
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Affiliation(s)
- Ping Wu
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Xiaoyu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Junxia Guo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Songli Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmiao Li
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China.
| | - Mei Zhang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Qingmao Fang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Bin Luo
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Hongsu Wang
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
| | - Weijin He
- Sichuan Academy of Traditional Chinese Medicine Sciences, Sichuan Genuine Medicinal Materials System Development Engineering Technology Research Center, Sichuan Key Laboratory of Quality and Innovation of Traditional Chinese Medicine, Chengdu, 610041, China
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Zheng G, Li W, Zhang S, Mi Q, Luo W, Zhao Y, Qin X, Li W, Pu S, Xu F. Multiomics strategies for decoding seed dormancy breakdown in Paris polyphylla. BMC PLANT BIOLOGY 2023; 23:247. [PMID: 37170087 PMCID: PMC10173654 DOI: 10.1186/s12870-023-04262-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND The disruption of seed dormancy is a complicated process and is controlled by various factors. Among these factors, membrane lipids and plant hormones are two of the most important ones. Paris polyphylla is an important Chinese herbaceous species, and the dormancy trait of its seed limits the cultivation of this herb. RESULTS In this study, we investigate the global metabolic and transcriptomic profiles of Paris polyphylla during seed dormancy breaking. Widely targeted metabolomics revealed that lysophospholipids (lysoPLs) increased during P. polyphylla seed dormancy breaking. The expression of phospholipase A2 (PLA2), genes correlated to the production of lysoPLs, up-regulated significantly during this process. Abscisic acid (ABA) decreased dramatically during seed dormancy breaking of P. polyphylla. Changes of different GAs varied during P. polyphylla seeds dormancy breaking, 13-OH GAs, such as GA53 were not detected, and GA3 decreased significantly, whereas 13-H GAs, such as GA15, GA24 and GA4 increased. The expression of CYP707As was not synchronous with the change of ABA content, and the expression of most UGTs, GA20ox and GA3ox up-regulated during seed dormancy breaking. CONCLUSIONS These results suggest that PLA2 mediated production of lysoPLs may correlate to the seed dormancy breaking of P. polyphylla. The conversion of ABA to ABA-GE catalysed by UGTs may be the main cause of ABA degradation. Through inhibition the expression of genes related to the synthesis of 13-OH GAs and up-regulation genes related to the synthesis of 13-H GAs, P. polyphylla synthesized more bioactive 13-H GA (GA4) to break its seed dormancy.
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Affiliation(s)
- Guowei Zheng
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Wenchun Li
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Shunzhen Zhang
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Qi Mi
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Wenxiu Luo
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yanli Zhao
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xiangshi Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Weijiao Li
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Shibiao Pu
- College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Furong Xu
- College of Ethnic Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Alam MS, Guan P, Zhu Y, Zeng S, Fang X, Wang S, Yusuf B, Zhang J, Tian X, Fang C, Gao Y, Khatun MS, Liu Z, Hameed HMA, Tan Y, Hu J, Liu J, Zhang T. Comparative genome analysis reveals high-level drug resistance markers in a clinical isolate of Mycobacterium fortuitum subsp . fortuitum MF GZ001. Front Cell Infect Microbiol 2023; 12:1056007. [PMID: 36683685 PMCID: PMC9846761 DOI: 10.3389/fcimb.2022.1056007] [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: 09/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Infections caused by non-tuberculosis mycobacteria are significantly worsening across the globe. M. fortuitum complex is a rapidly growing pathogenic species that is of clinical relevance to both humans and animals. This pathogen has the potential to create adverse effects on human healthcare. Methods The MF GZ001 clinical strain was collected from the sputum of a 45-year-old male patient with a pulmonary infection. The morphological studies, comparative genomic analysis, and drug resistance profiles along with variants detection were performed in this study. In addition, comparative analysis of virulence genes led us to understand the pathogenicity of this organism. Results Bacterial growth kinetics and morphology confirmed that MF GZ001 is a rapidly growing species with a rough morphotype. The MF GZ001 contains 6413573 bp genome size with 66.18 % high G+C content. MF GZ001 possesses a larger genome than other related mycobacteria and included 6156 protein-coding genes. Molecular phylogenetic tree, collinearity, and comparative genomic analysis suggested that MF GZ001 is a novel member of the M. fortuitum complex. We carried out the drug resistance profile analysis and found single nucleotide polymorphism (SNP) mutations in key drug resistance genes such as rpoB, katG, AAC(2')-Ib, gyrA, gyrB, embB, pncA, blaF, thyA, embC, embR, and iniA. In addition, the MF GZ001strain contains mutations in iniA, iniC, pncA, and ribD which conferred resistance to isoniazid, ethambutol, pyrazinamide, and para-aminosalicylic acid respectively, which are not frequently observed in rapidly growing mycobacteria. A wide variety of predicted putative potential virulence genes were found in MF GZ001, most of which are shared with well-recognized mycobacterial species with high pathogenic profiles such as M. tuberculosis and M. abscessus. Discussion Our identified novel features of a pathogenic member of the M. fortuitum complex will provide the foundation for further investigation of mycobacterial pathogenicity and effective treatment.
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Affiliation(s)
- Md Shah Alam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Yuting Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Sanshan Zeng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Shenzhen, China
| | - Buhari Yusuf
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Mst Sumaia Khatun
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
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Yang B, Sun S, Li S, Zeng J, Xu F. RNA-seq study reveals the signaling and carbohydrate metabolism regulators involved in dormancy release by warm stratification in Paris polyphylla var. yunnanensis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:355-365. [PMID: 37283615 PMCID: PMC10240920 DOI: 10.5511/plantbiotechnology.22.0824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/24/2022] [Indexed: 06/08/2023]
Abstract
Long-term seed dormancy of Paris polyphylla var. yunnanensis limits its large-scale artificial cultivation. It is crucial to understand the regulatory genes involving in dormancy release for artificial cultivation in this species. In this study, seed dormancy of Paris polyphylla var. yunnanensis was effectively released by warm stratification (20°C) for 90 days. The freshly harvested seeds (dormant) and stratified seeds (non-dormant) were used to sequence, and approximately 147 million clean reads and 28,083 annotated unigenes were detected. In which, a total of 10,937 differentially expressed genes (DEGs) were identified between dormant and non-dormant seeds. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) classification revealed that the majority unigenes involved in signaling transduction and carbohydrate metabolism. Of them, the signaling transduction-related DEGs were mainly hormones-, reactive oxygen species (ROS)-, and transcription factor (TF)-related genes. The largest number of signaling transduction-related DEGs were auxin-responsive genes (SAUR, AUX/IAA, and ARF) and AP2-like ethylene-responsive transcription factor (ERF/AP2). Moreover, at least 29 DEGs such as α-amylase (AMY), β-glucosidase (Bglb/Bglu/Bglx), and endoglucanase (Glu) were identified involving in carbohydrate metabolism. These identified genes provide a valuable resource to investigate the molecular basis of dormancy release in Paris polyphylla var. yunnanensis.
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Affiliation(s)
- Bin Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Shengyu Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiali Zeng
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Furong Xu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming 650500, China
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Dynamic RNA-Seq Study Reveals the Potential Regulators of Seed Germination in Paris polyphylla var. yunnanensis. PLANTS 2022; 11:plants11182400. [PMID: 36145801 PMCID: PMC9505804 DOI: 10.3390/plants11182400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Paris polyphylla var. yunnanensis is an important traditional Chinese medicine, but poor seed germination limits its large-scale artificial cultivation. Thus, it is crucial to understand the regulators of seed germination to obtain clues about how to improve the artificial cultivation of Paris polyphylla. In this study, the seeds at three germination stages, including ungerminated seeds (stage 1), germinated seeds with a 0.5 cm radicel length (stage 2), and germinated seeds with a 2.0 cm radicel length (stage 3) after warm stratification (20 °C) for 90 days were used for RNA sequencing. Approximately 220 million clean reads and 447,314 annotated unigenes were obtained during seed germination, of which a total of 4454, 5150, and 1770 differentially expressed genes (DEGs) were identified at stage 1 to stage 2, stage 1 to stage 3, and stage 2 to stage 3, respectively. Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and translation. Of them, several genes encoding the glutamate decarboxylase, glutamine synthetase, alpha-galactosidase, auxin-responsive protein IAA30, abscisic-acid-responsive element binding factor, mitogen-activated protein kinase kinase 9/18, and small and large subunit ribosomal proteins were identified as potentially involved in seed germination. The identified genes provide a valuable resource to study the molecular basis of seed germination in Paris polyphylla var. yunnanensis.
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Ling LZ, Zhang SD. Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis. PeerJ 2022; 10:e13304. [PMID: 35578673 PMCID: PMC9107301 DOI: 10.7717/peerj.13304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/29/2022] [Indexed: 01/13/2023] Open
Abstract
The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA3 level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA3/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA3/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis.
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Hua X, Song W, Wang K, Yin X, Hao C, Duan B, Xu Z, Su T, Xue Z. Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla. Commun Biol 2022; 5:50. [PMID: 35027659 PMCID: PMC8758714 DOI: 10.1038/s42003-022-03000-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/23/2021] [Indexed: 11/26/2022] Open
Abstract
The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges of OSC, CYP, and UGT genes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in P. polyphylla. This study provides an idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants. Xin Hua, Wei Song, and ZheYong Xue et al. report an effective method to predict key genes involved in polyphyllin biosynthesis in plants. Their results provide further insight into biosynthesis pathways in Paris polyphylla, and the approach may be relevant to other medicinal plants.
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Affiliation(s)
- Xin Hua
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Wei Song
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kangzong Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Xue Yin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Changqi Hao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Zhichao Xu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China. .,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China. .,National Engineering Research Center for Vegetables, Beijing, 100097, China.
| | - Zheyong Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China.
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Liao D, An R, Wei J, Wang D, Li X, Qi J. Transcriptome profiles revealed molecular mechanisms of alternating temperatures in breaking the epicotyl morphophysiological dormancy of Polygonatum sibiricum seeds. BMC PLANT BIOLOGY 2021; 21:370. [PMID: 34384392 PMCID: PMC8359049 DOI: 10.1186/s12870-021-03147-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/27/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND To adapt seasonal climate changes under natural environments, Polygonatum sibiricum seeds have a long period of epicotyl morphophysiological dormancy, which limits their wide-utilization in the large-scale plant progeny propagation. It has been proven that the controlled consecutive warm and cold temperature treatments can effectively break and shorten this seed dormancy status to promote its successful underdeveloped embryo growth, radicle emergence and shoot emergence. To uncover the molecular basis of seed dormancy release and seedling establishment, a SMRT full-length sequencing analysis and an Illumina sequencing-based comparison of P. sibiricum seed transcriptomes were combined to investigate transcriptional changes during warm and cold stratifications. RESULTS A total of 87,251 unigenes, including 46,255 complete sequences, were obtained and 77,148 unigenes (88.42%) were annotated. Gene expression analyses at four stratification stages identified a total of 27,059 DEGs in six pairwise comparisons and revealed that more differentially expressed genes were altered at the Corm stage than at the other stages, especially Str_S and Eme. The expression of 475 hormone metabolism genes and 510 hormone signaling genes was modulated during P. sibiricum seed dormancy release and seedling emergence. One thousand eighteen transcription factors and five hundred nineteen transcription regulators were detected differentially expressed during stratification and germination especially at Corm and Str_S stages. Of 1246 seed dormancy/germination known DEGs, 378, 790, and 199 DEGs were associated with P. sibiricum MD release (Corm vs Seed), epicotyl dormancy release (Str_S vs Corm), and the seedling establishment after the MPD release (Eme vs Str_S). CONCLUSIONS A comparison with dormancy- and germination-related genes in Arabidopsis thaliana seeds revealed that genes related to multiple plant hormones, chromatin modifiers and remodelers, DNA methylation, mRNA degradation, endosperm weakening, and cell wall structures coordinately mediate P. sibiricum seed germination, epicotyl dormancy release, and seedling establishment. These results provided the first insights into molecular regulation of P. sibiricum seed epicotyl morphophysiological dormancy release and seedling emergence. They may form the foundation of future studies regarding gene interaction and the specific roles of individual tissues (endosperm, newly-formed corm) in P. sibiricum bulk seed dormancy.
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Affiliation(s)
- Dengqun Liao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Ruipeng An
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
- College of Life Science, Hebei Agricultural University, Baoding, 071000, Hebei, China
- The Key Laboratory of Plant Physiology and Molecular Pathology, Hebei province, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Dongmei Wang
- College of Life Science, Hebei Agricultural University, Baoding, 071000, Hebei, China
- The Key Laboratory of Plant Physiology and Molecular Pathology, Hebei province, Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jianjun Qi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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11
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Gao JX, Chen YG, Li DS, Lin L, Liu Y, Li SH. Cloning and Functional Characterization of a Squalene Synthase from Paris polyphylla var. yunnanensis. Chem Biodivers 2021; 18:e2100342. [PMID: 34148286 DOI: 10.1002/cbdv.202100342] [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: 04/30/2021] [Accepted: 05/26/2021] [Indexed: 11/10/2022]
Abstract
Paris polyphylla Smith var. yunnanensis (Franch.) Hand. - Mazz. is a precious traditional Chinese medicine, and steroidal saponins are its major bioactive constituents possessing extensive biological activities. Squalene synthase (SQS) catalyzes the first dedicated step converting two molecular of farnesyl diphosphate (FDP) into squalene, a key intermediate in the biosynthetic pathway of steroidal saponins. In this study, a squalene synthase gene (PpSQS1) was cloned and functionally characterized from P. polyphylla var. yunnanensis, representing the first identified SQS from the genus Paris. The open reading frame of PpSQS1 is 1239 bp, which encodes a protein of 412 amino acids showing high similarity to those of other plant SQSs. Expression of PpSQS1 in Escherichia coli resulted in production of soluble recombinant proteins. Gas chromatography-mass spectrometry analysis showed that the purified recombinant PpSQS1 protein could produce squalene using FDP as a substrate in the in vitro enzymatic assay. qRT-PCR analysis indicated that PpSQS1 was highly expressed in rhizomes, consistent with the dominant accumulation of steroidal saponins there, suggesting that PpSQS1 is likely involved in the biosynthesis of steroidal saponins in the plant. The findings lay a foundation for further investigation on the biosynthesis and regulation of steroidal saponins, and also provide an alternative gene for manipulation of steroid production using synthetic biology.
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Affiliation(s)
- Jian-Xiong Gao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yue-Gui Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - De-Sen Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Lin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Yan Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
| | - Sheng-Hong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, P. R. China
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12
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Liu TH, Zhou Y, Tao WC, Liu Y, Zhang XM, Tian SZ. Bacterial Diversity in Roots, Stems, and Leaves of Chinese Medicinal Plant Paris polyphylla var. yunnanensis. Pol J Microbiol 2020; 69:91-97. [PMID: 32189484 PMCID: PMC7256839 DOI: 10.33073/pjm-2020-012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/02/2020] [Accepted: 02/13/2020] [Indexed: 11/05/2022] Open
Abstract
The root of Paris polyphylla var. yunnanensis, a famous and endangered traditional Chinese herb, has a significant medicinal value. The aim of this study was to analyze the composition and functional characteristics of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis. The 16S rRNA gene sequencing and functional prediction of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis were conducted. The Chao and Shannon indices of the bacteria in roots were significantly higher than those in stems and leaves. The dominant endophyte phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The main genera detected in roots were unclassified Cyanobacteria, Rhizobium, Flavobacterium, and Sphingobium; the main genera in stems were norank_c__Cyanobacteria, Bacillus, and Pseudomonas; the main genera in leaves were norank_c__Cyanobacteria and Rhizobium. The microbiota in roots was particularly enriched in functional categories "extracellular structures" and "cytoskeleton" compared with stems and leaves (p < 0.05). Our study reveals the structural and functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis, which aids in the scientific understanding of this plant. The root of Paris polyphylla var. yunnanensis, a famous and endangered traditional Chinese herb, has a significant medicinal value. The aim of this study was to analyze the composition and functional characteristics of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis. The 16S rRNA gene sequencing and functional prediction of bacterial endophytes in roots, stems, and leaves of P. polyphylla var. yunnanensis were conducted. The Chao and Shannon indices of the bacteria in roots were significantly higher than those in stems and leaves. The dominant endophyte phyla were Cyanobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The main genera detected in roots were unclassified Cyanobacteria, Rhizobium, Flavobacterium, and Sphingobium; the main genera in stems were norank_c__Cyanobacteria, Bacillus, and Pseudomonas; the main genera in leaves were norank_c__Cyanobacteria and Rhizobium. The microbiota in roots was particularly enriched in functional categories “extracellular structures” and “cytoskeleton” compared with stems and leaves (p < 0.05). Our study reveals the structural and functional characteristics of the endophytic bacteria in roots, stems, and leaves of P. polyphylla var. yunnanensis, which aids in the scientific understanding of this plant.
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Affiliation(s)
- Tian-Hao Liu
- Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine , Kunming, Yunnan , China ; College of Chinese Medicine, Jinan University , Guangzhou, Guangdong , China
| | - Yin Zhou
- Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine , Kunming, Yunnan , China
| | - Wen-Cong Tao
- College of Chinese Medicine, Jinan University , Guangzhou, Guangdong , China
| | - Yang Liu
- Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine , Kunming, Yunnan , China
| | - Xiao-Mei Zhang
- Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine , Kunming, Yunnan , China
| | - Shou-Zheng Tian
- Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine , Kunming, Yunnan , China
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13
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Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus. BIOMED RESEARCH INTERNATIONAL 2020; 2019:1864168. [PMID: 31915684 PMCID: PMC6935459 DOI: 10.1155/2019/1864168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/28/2019] [Indexed: 01/19/2023]
Abstract
Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p ≤ 0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.
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14
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Yang K, Yang L, Fan W, Long GQ, Xie SQ, Meng ZG, Zhang GH, Yang SC, Chen JW. Illumina-based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after-ripening process. PHYSIOLOGIA PLANTARUM 2019; 167:597-612. [PMID: 30548605 DOI: 10.1111/ppl.12904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/28/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Panax notoginseng (Burk) F.H. Chen is an economically and medicinally important plant of the family Araliacease, with seed dormancy being a key factor limiting the extended cultivation of P. notoginseng. The seeds belong to the morphophysiological dormancy (MPD) group, and it has also been described as the recalcitrant seed. To date, the molecular mechanism of dormancy release in the recalcitrant seed of P. notoginseng is unknown. In the present study, the transcript profiles of seeds from different after-ripening stages (0, 20, 40 and 60 days) were investigated using Illumina Hiseq 2500 technology. 91 979 946 clean reads were generated, and 81 575 unigenes were annotated in at least one database. In addition, the differentially expressed genes (DEGs) were identified by the pairwise comparisons. We screened out 2483 DEGs by the three key groups of 20 days vs 0 d, 40 d vs 0 d and 60 d vs 0 d. The DEGs were analyzed by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Meanwhile, we obtained 78 DEGs related to seeds dormancy release at different after-ripening stages of P. notoginseng, of which 15 DEGs were associated with abscisic acid and gibberellin. 26 DEGs that encode late embryogenesis abundant protein and antioxidant enzyme were correlated with desiccation tolerance in seeds. In summary, the results obtained here showed that PECTINESTERASE-2-LIKE, GA-INSENSITIVE, ENT-KAURENE SYNTHASE, PROTEIN PHOSPHATASE 2C, GIBBERELLIN 2-BETA-DIOXYGENASE, SUPEROXIDE DISMUTASE, L-ASCORBATE PEROXIDASE, CATALASE, LATE EMBRYOGENESIS ABUNDANT PROTEIN DC3 and DEHYDRIN 9 were potentially involved in dormancy release and desiccation sensitivity of P. notoginseng seeds. The data might provide a basis for researches on MPD.
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Affiliation(s)
- Kai Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Ling Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Fan
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guang-Qiang Long
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Shi-Qing Xie
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhen-Gui Meng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guang-Hui Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Sheng-Chao Yang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Wen Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
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15
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Multi-source information fusion strategies of aerial parts in FTIR-ATR spectroscopic characterization and classification of Paris polyphylla var. yunnanensis. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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16
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In-silico identification and analysis of miRNAs from germinating seeds in Paris polyphylla var. yunnanensis by deep sequencing. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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17
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Pei Y, Zhang Q, Wang Y. Application of Authentication Evaluation Techniques of Ethnobotanical Medicinal Plant Genus Paris: A Review. Crit Rev Anal Chem 2019; 50:405-423. [DOI: 10.1080/10408347.2019.1642734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- Yifei Pei
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Qingzhi Zhang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Yuanzhong Wang
- Institute of Medicinal Plants, Yunnan Academy of Agricultural Sciences, Kunming, China
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18
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Comparative analysis of proteomic and metabolomic profiles of different species of Paris. J Proteomics 2019; 200:11-27. [PMID: 30890455 DOI: 10.1016/j.jprot.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/12/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants. SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
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Comparative transcriptomic analysis reveals genes regulating the germination of morphophysiologically dormant Paris polyphylla seeds during a warm stratification. PLoS One 2019; 14:e0212514. [PMID: 30789936 PMCID: PMC6383930 DOI: 10.1371/journal.pone.0212514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/04/2019] [Indexed: 01/18/2023] Open
Abstract
We previously analyzed the expression of genes associated with Paris polyphylla var. yunnanensis seed maturation and dormancy release; however, we were unable to clarify the relationship between gene expression levels and these processes. To reveal the molecular mechanisms underlying P. polyphylla var. yunnanensis seed dormancy release during a warm stratification, the transcriptomes of dormant and germinating P. polyphylla var. yunnanensis seeds were separately analyzed by RNA sequencing and were also compared with the transcriptomes of stem-leaf and root tissues harvested during the seed maturation stage. The RNA sequencing of five tissues generated 234,331 unigenes, of which 10,137 (4.33%) were differentially expressed among the analyzed tissues. The 6,619 unigenes whose expression varied among mature dormant, sprouted, and germinated seeds included 95 metabolic and 62 signaling genes related to abscisic acid, gibberellin, auxin, brassinosteroid, cytokinin, ethylene, jasmonic acid and salicylic acid. Additionally, 243 differentially expressed genes were annotated as known seed dormancy/germination-related genes. Among these genes, 109 were regulated by hormones or involved in hormone signal transduction. Finally, 310 transcription factor unigenes, including 71 homologs of known seed dormancy/ germination-related genes, were observed to be differentially expressed during a warm stratification. These results confirm that multiple hormones and transcription factors influence P. polyphylla var. yunnanensis seed dormancy release and germination during a warm stratification. This study identified candidate genes (e.g., ABI5) that should be cloned and functionally characterized regarding their effects on the release of P. polyphylla var. yunnanensis seed morphophysiological dormancy.
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20
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Ma Y, Chen X, Guo B. Identification of genes involved in metabolism and signalling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy. PLANT CELL REPORTS 2018; 37:1061-1075. [PMID: 29796945 DOI: 10.1007/s00299-018-2291-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 05/04/2018] [Indexed: 06/08/2023]
Abstract
Key genes involved in metabolism and signalling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy release were identified using phytochemistry, transcriptomics, and bioinformatic methods. The molecular mechanism of seed morphophysiological dormancy of Epimedium pseudowushanense B.L.Guo. remains largely unknown. The endogenous abscisic acid (ABA) and gibberellin (GA) content of E. pseudowushanense seeds at three developmental stages were quantitatively determined. The results showed the levels of ABA in E. pseudowushanense seeds decreased during seed embryo growth and development, while levels of GA3 increased during seed embryo growth, and levels of GA4 increased during seed dormancy release and seed sprouting. A high-throughput sequencing method was used to determine the E. pseudowushanense seed transcriptome. The transcriptome data were assembled as 178,613 unigenes and the numbers of differentially expressed unigenes between the seed development stages were compared. Computer analysis of reference pathways revealed that 12 candidate genes were likely to be involved in metabolism and signalling of ABA and GAs. The expression patterns of these genes were revealed by real-time quantitative PCR. Phylogenetic relationships among the deduced E. pseudowushanense proteins and their homologous proteins in other plant species were analysed. The results indicated that EpNCED1, EpNCED2, EpCYP707A1, and EpCYP707A2 are likely to be involved in ABA biosynthesis and catabolism. EpSnRK2 is likely implicated in ABA signalling during seed dormancy. EpGA3ox is likely to be involved in GA biosynthesis. EpDELLA1 and EpDELLA2 are likely implicated in GA signalling. This study is the first to provide the E. pseudowushanense seed transcriptome and the key genes involved in metabolism and signalling of ABA and GAs, and it is valuable for studies on the mechanism of seed morphophysiological dormancy.
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Affiliation(s)
- Yimian Ma
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Xiangdong Chen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
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Enhancement of Nucleoside Production in Hirsutella sinensis Based on Biosynthetic Pathway Analysis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2520347. [PMID: 29333435 PMCID: PMC5733210 DOI: 10.1155/2017/2520347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/25/2017] [Indexed: 11/18/2022]
Abstract
To enhance nucleoside production in Hirsutella sinensis, the biosynthetic pathways of purine and pyrimidine nucleosides were constructed and verified. The differential expression analysis showed that purine nucleoside phosphorylase, inosine monophosphate dehydrogenase, and guanosine monophosphate synthase genes involved in purine nucleotide biosynthesis were significantly upregulated 16.56-fold, 8-fold, and 5.43-fold, respectively. Moreover, dihydroorotate dehydrogenase, uridine nucleosidase, uridine/cytidine monophosphate kinase, and inosine triphosphate pyrophosphatase genes participating in pyrimidine nucleoside biosynthesis were upregulated 4.53-fold, 10.63-fold, 4.26-fold, and 5.98-fold, respectively. To enhance the nucleoside production, precursors for synthesis of nucleosides were added based on the analysis of biosynthetic pathways. Uridine and cytidine contents, respectively, reached 5.04 mg/g and 3.54 mg/g when adding 2 mg/mL of ribose, resulting in an increase of 28.6% and 296% compared with the control, respectively. Meanwhile, uridine and cytidine contents, respectively, reached 10.83 mg/g 2.12 mg/g when adding 0.3 mg/mL of uracil, leading to an increase of 176.3% and 137.1%, respectively. This report indicated that fermentation regulation was an effective way to enhance the nucleoside production in H. sinensis based on biosynthetic pathway analysis.
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Ling LZ, Zhang SD, Zhao F, Yang JL, Song WH, Guan SM, Li XS, Huang ZJ, Cheng L. Transcriptome-Wide Identification and Prediction of miRNAs and Their Targets in Paris polyphylla var. yunnanensis by High-Throughput Sequencing Analysis. Int J Mol Sci 2017; 18:ijms18010219. [PMID: 28117746 PMCID: PMC5297848 DOI: 10.3390/ijms18010219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 01/08/2023] Open
Abstract
Long dormancy period of seeds limits the large-scale artificial cultivation of the scarce Paris polyphylla var. yunnanensis, an important traditional Chinese medicine. Characterizing miRNAs and their targets is crucial to understanding the role of miRNAs during seed dormancy in this species. Considering the limited genome information of this species, we first sequenced and assembled the transcriptome data of dormant seeds and their seed coats as the reference genome. A total of 146,671 unigenes with an average length of 923 bp were identified and showed functional diversity based on different annotation methods. Two small RNA libraries from respective seeds and seed coats were sequenced and the combining data indicates that 263 conserved miRNAs belonging to at least 83 families and 768 novel miRNAs in 1174 transcripts were found. The annotations of the predicted putative targets of miRNAs suggest that these miRNAs were mainly involved in the cell, metabolism and genetic information processing by direct and indirect regulation patterns in dormant seeds of P. polyphylla var. yunnanensis. Therefore, we provide the first known miRNA profiles and their targets, which will assist with further study of the molecular mechanism of seed dormancy in P. polyphylla var. yunnanensis.
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Affiliation(s)
- Li-Zhen Ling
- BGI-Yunnan, Kunming 650106, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Fan Zhao
- BGI-Yunnan, Kunming 650106, China.
| | | | | | | | | | | | - Le Cheng
- BGI-Yunnan, Kunming 650106, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
- College of Clinical Medicine, College of Basic Medical Sciences, Dali University, Dali 671000, China.
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Enhancement of cordyceps polysaccharide production via biosynthetic pathway analysis in Hirsutella sinensis. Int J Biol Macromol 2016; 92:872-880. [DOI: 10.1016/j.ijbiomac.2016.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/30/2016] [Accepted: 08/01/2016] [Indexed: 11/21/2022]
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Sharma A, Kalita P, Tag H. Distribution and phytomedicinal aspects of Paris polyphylla Smith from the Eastern Himalayan Region: A review. ACTA ACUST UNITED AC 2015. [DOI: 10.5667/tang.2015.0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq. PLoS One 2015; 10:e0118558. [PMID: 25790114 PMCID: PMC4366157 DOI: 10.1371/journal.pone.0118558] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 01/20/2015] [Indexed: 01/04/2023] Open
Abstract
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15–20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.
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