1
|
Javan SL, Kashkooli AB, Shojaeiyan A, Majidian S. Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek. BMC Genomics 2024; 25:390. [PMID: 38649807 PMCID: PMC11034138 DOI: 10.1186/s12864-024-10253-x] [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: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the medicinal plants traditionally used in human nutrition and medicine which contains an active substance, called diosgenin, with anticancer properties. Biosynthesis of this important anticancer compound in fenugreek can be enhanced using eliciting agents which involves in manipulation of metabolite and biochemical pathways stimulating defense responses. Methyl jasmonate elicitor was used to increase diosgenin biosynthesis in fenugreek plants. However, the molecular mechanism and gene expression profiles underlying diosgening accumulation remain unexplored. In the current study we performed an extensive analysis of publicly available RNA-sequencing datasets to elucidate the biosynthesis and expression profile of fenugreek plants treated with methyl jasmonate. For this purpose, seven read datasets of methyl jasmonate treated plants were obtained that were covering several post-treatment time points (6-120 h). Transcriptomics analysis revealed upregulation of several key genes involved in diosgenein biosynthetic pathway including Squalene synthase (SQS) as the first committed step in diosgenin biosynthesis as well as Squalene Epoxidase (SEP) and Cycloartenol Synthase (CAS) upon methyl jasmonate application. Bioinformatics analysis, including gene ontology enrichment and pathway analysis, further supported the involvement of these genes in diosgenin biosynthesis. The bioinformatics analysis led to a comprehensive validation, with expression profiling across three different fenugreek populations treated with the same methyl jasmonate application. Initially, key genes like SQS, SEP, and CAS showed upregulation, followed by later upregulation of Δ24, suggesting dynamic pathway regulation. Real-time PCR confirmed consistent upregulation of SQS and SEP, peaking at 72 h. Additionally, candidate genes Δ24 and SMT1 highlighted roles in directing metabolic flux towards diosgenin biosynthesis. This integrated approach validates the bioinformatics findings and elucidates fenugreek's molecular response to methyl jasmonate elicitation, offering insights for enhancing diosgenin yield. The assembled transcripts and gene expression profiles are deposited in the Zenodo open repository at https://doi.org/10.5281/zenodo.8155183 .
Collapse
Affiliation(s)
- Sara Lamei Javan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | | | - AbdolAli Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Switzerland SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
2
|
Yadav S, Kumari R, Rangan P, Gaikwad AB. Variability in genome size of Trigonella foenum-graecum, Trigonella corniculata and Trigonella caerulea as estimated by flow cytometry indicates complex evolutionary history of fenugreek. Mol Biol Rep 2024; 51:489. [PMID: 38578370 DOI: 10.1007/s11033-024-09417-5] [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: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The determination of genome size is a fundamental step which provides a basis to initiate studies aimed at deciphering the genetic similarity of a species and to carry out other genomics based investigations. Fenugreek (Trigonella spp.) is an important spice crop which has numerous health promoting phytochemicals. Many species within this genus are known for their various health benefits owing to the presence of a wide diversity of important phytochemicals like diosgenin, trigonelline, fenugreekine, galactomannan, 4-hydroxy isoleucine, etc. It is a multipurpose crop being cultivated for food, animal feed and industrial purposes. Despite its importance, research on the genomics aspect of fenugreek remains scant. In the absence of sufficient genomic information, crop improvement in fenugreek is severely lagging. METHODS AND RESULTS Estimation of genome size of a species is the preliminary step for initiation of any genomic studies and therefore in the present study we have estimated the genome size for fenugreek. Here, we have determined the genome sizes of three different Trigonella spp. namely T. foenum-graecum, T. corniculata and T. caerulea through flow cytometry (FC). The 2 C DNA content values were found to be 6.05 pg (T. foenum-graecum), 1.83 pg (T. corniculata) and 1.96 pg (T. caerulea). The genome size of T. foenum-graecum is approximately three times the genome size of T. corniculata and T. caerulea. This variation in genome size of more than three-fold indicates the level of genetic divergence among the three species, though within the same genus. CONCLUSIONS The differences observed in the genome sizes of the three species provide conclusive evidence of their genetic divergence. Additionally, the information about the genome size would provide an impetus to the structural and functional genomics-based research in this crop.
Collapse
Affiliation(s)
- Sheel Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Ratna Kumari
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Parimalan Rangan
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Ambika Baldev Gaikwad
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
| |
Collapse
|
3
|
Zhao Q, Wu G, Yang P, Shi Y, Fu Z, Mo H, Shi C, Yu S. Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds. Genes (Basel) 2024; 15:343. [PMID: 38540402 PMCID: PMC10969933 DOI: 10.3390/genes15030343] [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: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 06/14/2024] Open
Abstract
Fenugreek (Trigonella foenum-graecum L.) is a traditional medicinal plant for treating human diseases that is widely cultivated in many countries. However, the component and related metabolic pathways are still unclear. To understand the changes in expression of the component and related genes during seed development, this study employed metabolomic and transcriptomic analyses and integrative analysis to explore the metabolites and pathways involved in the growth of fenugreek. The antifungal activity of the fenugreek seeds was also analyzed. A total of 9499 metabolites were identified in the positive ion mode, and 8043 metabolites were identified in the negative ion mode. Among them, the main components were fatty acyls, prenol lipids, steroids, steroid derivatives, flavonoids, and isoflavonoids. Among these enriched pathways, the top 20 pathways were "flavone and flavonol biosynthesis", "isoflavonoid biosynthesis", and "flavonoid biosynthesis". 3,7-Di-O-methylquercetin, flavonoids, pseudobaptigenin, isoflavonoids, methylecgonine, alkaloids, and derivatives were the most significantly upregulated metabolites. There were 38,137 differentially expressed genes (DEGs) identified via transcriptomic analysis. According to the KEGG pathway enrichment analysis, 147 DEGs were significantly enriched in "flavonoid biosynthesis". Ten DEGs of the six key enzymes were found to be involved in three pathways related to flavonoid and alkaloid synthesis in fenugreek. The antifungal activity test revealed the inhibitory effect of the ethanol extract of fenugreek seeds on Alternaria tenuissima (Kunze)Wiltshire and Magnaporthe oryzae. These findings further prove that the use of botanical pesticides in fenugreek fruit has research value.
Collapse
Affiliation(s)
- Qiuyu Zhao
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China;
| | - Guoxing Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (G.W.); (C.S.)
| | - Pu Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (P.Y.); (Y.S.); (Z.F.); (H.M.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Yuanchong Shi
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (P.Y.); (Y.S.); (Z.F.); (H.M.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Zuoyi Fu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (P.Y.); (Y.S.); (Z.F.); (H.M.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Haifeng Mo
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (P.Y.); (Y.S.); (Z.F.); (H.M.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Chunlan Shi
- College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (G.W.); (C.S.)
| | - Shuhui Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China;
| |
Collapse
|
4
|
Kumar A, Singh N, Joshi R. Deciphering the metabolic signatures of Trigonella microgreens as a function of photoperiod and temperature using targeted compound analysis and non-targeted UHPLC-QTOF-IMS based approach. Food Res Int 2024; 176:113834. [PMID: 38163730 DOI: 10.1016/j.foodres.2023.113834] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Trigonella foenum-graecum L. (Fenugreek) is an annual herb that belongs to Fabaceae family. The compositional make-up of microgreens depends on prevailing environmental conditions. So, Trigonella microgreens were cultivated under different photoperiod and temperature conditions and evaluated for plant height, total chlorophyll content (TCC), targeted compound analysis and non-targeted UHPLC-QTOF-IMS based metabolomic profile. The plant height and TCC of Trigonella microgreens increased by approximately 22 % and 20 %, respectively under T1 conditions (longer photoperiod of 22 h with 22 °C in light and 17 °C in dark). The targeted phenolic profile analysis revealed the dominant presence of gallic acid, p-coumaric acid and apigenin in Trigonella microgreens. Also, the concentration of p-coumaric acid concentration raised from 3.51 mg/g to 5.83 mg/g as a response of T1 conditions. The sugar profile revealed augmented concentration of myo-inositol, glucose, fructose, xylose, maltose, and sucrose in longer photoperiod with T1 conditions. The microgreens were also rich in amino acids like aspartic acid, glutamic acid, leucine, isoleucine, and phenylalanine. Notably, the concentration of proline increased from 10.40 mg/g to 16.92 mg/g as a response to T1 growth conditions. The concentration of these metabolites varied significantly under different photoperiod and temperature conditions. The comprehensive non-targeted UHPLC-QTOF-IMS analysis of microgreens revealed different class of metabolites like organic compounds, alkaloids, coumarin-derivatives, phenolic and flavonoid derivatives, terpenoids, sugars, amino acids and few nucleic acid derivatives. The multivariate PLS-DA explained different expression level of metabolites under different growing conditions. The T1 growing condition resulted in the increased biosynthesis of phenolic compounds and various metabolites. The expression level of terpenoid derivatives specifically of Trigonelloside C and Trigoneoside XIIa/b increased under T1 conditions. The substantial alteration in the metabolites due to growing conditions may alter the microgreen's dietary benefits. So, additional research may be warranted.
Collapse
Affiliation(s)
- Arun Kumar
- Department of Food Science and Technology, Guru Nanak Dev University, Amritsar 143005, Punjab, India; Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun 248002, India
| | - Narpinder Singh
- Department of Food Science and Technology, Graphic Era Deemed to be University, Dehradun 248002, India.
| | - Robin Joshi
- Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, University of Pennsylvania (UPenn), Philadelphia, PA 19104, USA; Biotechnology Division, CSIR- Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.
| |
Collapse
|
5
|
Lu J. Genome-Wide Comparative Profiles of Triterpenoid Biosynthesis Genes in Ginseng and Pseudo Ginseng Medicinal Plants. Life (Basel) 2023; 13:2227. [PMID: 38004367 PMCID: PMC10672587 DOI: 10.3390/life13112227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Saponin-rich medicinal plants, particularly ginseng and Pseudo ginseng, are valuable in traditional medical practice due to the presence of different saponins. These plants benefit from natural saponins/triterpenoids drugs, such as Ginsenosides, Gypenosides, Platycodins, and Lancemasides. Ginsenosides are highly required for research and functional materials preparation in industrial practices, and some compounds, like Compound-K, have been taken to human trials for various therapeutic applications. To elucidate the genes/transcripts profiles responsible for secondary metabolites and ginsenoside biosynthesis in Ginseng and Pseudo ginseng plant genomes, a comparative analysis was conducted in this study. Nine plant genomes with a 99% BUSCO completeness score were used, resulting in 49 KEGG secondary metabolite pathways, 571 cytochromes genes with 42 families, and 3529 carbohydrate genes with 103 superfamilies. The comparative analysis revealed 24 genes/transcripts belonging to the CYP716 family, which is involved in the ginsenoside biosynthesis pathway. Additionally, it found that various ginsenosides demonstrated strong binding affinity with twelve targets, with ginsenoside Rg3, Rg2, Rh1, Rh5, F3, Rh9, Panaxadione, Protopanaxatriol, Floral ginsenoside C, and Floral ginsenoside E exhibiting the highest binding affinities with the tested enzymes. Since these groups of enzymes are not yet fully characterized for Pseudo ginseng plants in the interconversion of triterpenoids, this comparative bioinformatics analysis could aid experimentalists in selecting and conducting characterization with practical knowledge.
Collapse
Affiliation(s)
- Jing Lu
- Division of General Education, Seokyeong University, Seoul 02173, Republic of Korea
| |
Collapse
|
6
|
Parwez R, Aqeel U, Aftab T, Khan MMA, Naeem M. Melatonin supplementation combats nickel-induced phytotoxicity in Trigonella foenum-graecum L. plants through metal accumulation reduction, upregulation of NO generation, antioxidant defence machinery and secondary metabolites. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107981. [PMID: 37639982 DOI: 10.1016/j.plaphy.2023.107981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
Nickel (Ni) at a toxic level (80 mg kg-1 of soil) adversely affects the crop performance of fenugreek (Trigonella foenum-graecum L.). Melatonin (MEL), a potent plant growth regulator, is ascribed to offer promising roles in heavy metal stress alleviation. In this study, different doses viz. 0, 25, 50, 75 and 100 μM of MEL were administered to plants through foliage under normal and Ni-stress conditions. The experiment unveiled positive roles of MEL in enhancing root-shoot lengths, fresh-dry weights, seed yield and restoring photosynthetic efficiency assessed in terms of higher Fv/Fm, YII, qP, and lower NPQ values in plants exposed to Ni (80 mg kg-1). MEL supplementation (at 75 μM) effectively restricted Ni accumulation and regulated oxidative stress via modulation of MDA, O2-, H2O2 and NO generation, most prominently. Besides, MEL at 75 μM more conspicuously perked up the activities of antioxidant enzymes like SOD, POX, CAT and APX by 15.7, 20.0, 14.5 and 16.5% higher than the Ni-exposed plants for effective ROS scavenging. Likewise, MEL at 75 μM also efficiently counteracted Ni-generated osmotic stress, through an upscaled accumulation of proline (19.6%) along with the enhancement in the concentration of total phenols (13.6%), total tannins (11.2%), total flavonoids (25.5%) and total alkaloids (19.2%) in plant's leaves. Furthermore, under 80 mg kg-1 Ni stress, MEL at 75 μM improved the seed's trigonelline content by 40.1% higher compared to Ni-disturbed plants, upgrading the pharmacological actions of the plant. Thus, the present study deciphers the envisaged roles of MEL in the alleviation of Ni stress in plants to enhance overall crop productivity.
Collapse
Affiliation(s)
- Rukhsar Parwez
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Umra Aqeel
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - Tariq Aftab
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - M Masroor A Khan
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India
| | - M Naeem
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, India.
| |
Collapse
|
7
|
Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
Collapse
Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| |
Collapse
|