1
|
Samaratunga R, Kantono K, Kam R, Gannabathula S, Hamid N. Microencapsulated Asiatic Pennywort (Centella asiatica) fortified chocolate oat milk beverage: Formulation, polyphenols content, and consumer acceptability. J Food Sci 2024. [PMID: 39138633 DOI: 10.1111/1750-3841.17277] [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: 03/09/2024] [Revised: 06/19/2024] [Accepted: 07/11/2024] [Indexed: 08/15/2024]
Abstract
This study investigated the use of microencapsulated Asiatic pennywort (Centella asiatica) (CA) as a functional ingredient to formulate a novel chocolate oat milk beverage. The main objectives of the study were to characterize and encapsulate bioactive components from CA and to determine the polyphenol content and sensory properties of the beverage. CA extract was microencapsulated using maltodextrin and gum Arabic as carriers and subsequently freeze-dried to produce microcapsules. Microencapsulated CA was incorporated into chocolate oat milk at varying concentrations. Polyphenol content of the beverages was quantified using liquid chromatography-mass spectrometry. Consumer acceptability and sensory perception of the beverages were evaluated through an acceptance test and a check-all-that-apply test, respectively, to assess the sensory characteristics of the chocolate oat milk beverage. CA fortified chocolate oat milk contained fourteen polyphenols. Increasing the concentration of microencapsulated CA led to an increase in the polyphenol content of the beverage. Among the identified polyphenols, asiatic acid and asiaticoside stood out as the unique and most abundant compounds in CA (p < 0.05). Additionally, the incorporation of cocoa powder into the beverage further contributed to the polyphenol content, introducing bioactive compounds such as benzoic acid, caffeic acid, catechin, chlorogenic acid, kaempferol, luteolin, madecassic acid, p-coumaric acid, and quercetin. Evaluation of consumer acceptability revealed that chocolate oat milk beverages containing 2% and 4% microencapsulated CA were liked by consumers. However, beverages with higher concentrations of CA were perceived as less acceptable, characterized by grassy, bitter, and earthy attributes. In conclusion, this study demonstrates the potential of microencapsulated CA as a functional ingredient in chocolate oat milk beverages. PRACTICAL APPLICATION: This study reveals new insights on the microencapsulation of bioactive compounds in CA, proposing its potential as a novel functional ingredient in food and beverage applications in Western markets. The study revealed microencapsulated CA retained polyphenols in CA including asiatic acid and asiaticoside responsible for its bioactive properties. Consumer perception of CA added to oat milk revealed that it can be added at an acceptable level of 4%; however, higher amounts can decrease consumer acceptability. As practitioners explore the incorporation of CA as a functional component in food products, it is crucial to explore preservation techniques for the sensitive bioactive components while balancing the optimal amount of CA to enhance overall consumer liking.
Collapse
Affiliation(s)
- Roselle Samaratunga
- Centre for Future Foods, Auckland University of Technology, Auckland, New Zealand
| | - Kevin Kantono
- Centre for Future Foods, Auckland University of Technology, Auckland, New Zealand
| | - Rothman Kam
- Centre for Future Foods, Auckland University of Technology, Auckland, New Zealand
| | - Swapna Gannabathula
- Centre for Future Foods, Auckland University of Technology, Auckland, New Zealand
| | - Nazimah Hamid
- Centre for Future Foods, Auckland University of Technology, Auckland, New Zealand
| |
Collapse
|
2
|
Prashant SP, Bhawana M. An update on biotechnological intervention mediated by plant tissue culture to boost secondary metabolite production in medicinal and aromatic plants. PHYSIOLOGIA PLANTARUM 2024; 176:e14400. [PMID: 38945697 DOI: 10.1111/ppl.14400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 07/02/2024]
Abstract
Since prehistoric times, medicinal and aromatic plants (MAPs) have been employed for various therapeutic purposes due to their varied array of pharmaceutically relevant bioactive compounds, i.e. secondary metabolites. However, when secondary metabolites are isolated directly from MAPs, there is occasionally very poor yield and limited synthesis of secondary metabolites from particular tissues and certain developmental stages. Moreover, many MAPs species are in danger of extinction, especially those used in pharmaceuticals, as their natural populations are under pressure from overharvesting due to the excess demand for plant-based herbal remedies. The extensive use of these metabolites in a number of industrial and pharmaceutical industries has prompted a call for more research into increasing the output via optimization of large-scale production using plant tissue culture techniques. The potential of plant cells as sources of secondary metabolites can be exploited through a combination of product recovery technology research, targeted metabolite production, and in vitro culture establishment. The plant tissue culture approach provides low-cost, sustainable, continuous, and viable secondary metabolite production that is not affected by geographic or climatic factors. This study covers recent advancements in the induction of medicinally relevant metabolites, as well as the conservation and propagation of plants by advanced tissue culture technologies.
Collapse
Affiliation(s)
- Shera Pandit Prashant
- Department of Environmental Sciences, Central University of Himachal Pradesh (CUHP), Kangra, Shahpur, Himachal Pradesh
| | - Mishra Bhawana
- Department of Environmental Sciences, Central University of Himachal Pradesh (CUHP), Kangra, Shahpur, Himachal Pradesh
| |
Collapse
|
3
|
Afroz S, Khatoon K, Warsi Z, Husain Z, Kumar Verma S, Ur Rahman L. Molecular cloning and heterologous expression analysis of 1-Deoxy-D-Xylulose-5-Phosphate Synthase gene in Centella asiatica L. Gene 2024; 895:148015. [PMID: 37984537 DOI: 10.1016/j.gene.2023.148015] [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: 08/09/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
Abstract
Many genes involved in triterpenoid saponins in plants control isoprenoid flux and constitute the precursor pool, which is channeled into various downstream pathways leading to the synthesis of triterpenoid saponins in C. asiatica. Full-length 1-Deoxy-D-Xylulose-5-Phosphate-Synthase (CaDXS) gene was isolated for the study from the previously annotated Centella asiatica leaves transcriptomic data. The CaDXS gene sequence was submitted to the NCBI databases with GenBank accession number MZ997832. The full-length CaDXS gene contained a 2244 base pair open reading frame that encoded a 747 amino acid polypeptide. The predicted molecular weight (MW) and theoretical pI of DXS are 76.28 kDa and 6.86, respectively. Multiple amino acid sequence alignment of amino acids and phylogenetic studies suggest that CaDXS shares high similarities with DXS from other plants DXS belonging to different families. A phylogenetic tree was constructed using Molecular Evolutionary Genetic Analysis (MEGA) version 10.1.6. Structural analysis provided fundamental information about the three-dimensional features and physicochemical parameters of the CaDXS protein. Quantitative expression analysis showed that CaDXS transcripts were maximally expressed in leaf, followed by petiole, roots, and node tissues. CaDXS was cloned into the expression vector pET28a, expressed heterologously in DH5α bacteria, confirmed by sequencing, and subsequently characterized by protein expression and functional complementation. The study focused on understanding the protein structure, biological significance, regulatory mechanism, functional analysis, and gene characterization of the centellosides biosynthetic pathway gene DXS for the first time in the plant. It would provide new information about the metabolic pathway and its relative contribution to isoprenoid biosynthesis.
Collapse
Affiliation(s)
- Shama Afroz
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India
| | - Kahkashan Khatoon
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Zafar Warsi
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Zakir Husain
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India
| | - Sanjeet Kumar Verma
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India
| | - Laiq Ur Rahman
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226022, India.
| |
Collapse
|
4
|
Li M, Lu Y, Gao Z, Yue D, Hong J, Wu J, Xi D, Deng W, Chong Y. Pan-Omics in Sheep: Unveiling Genetic Landscapes. Animals (Basel) 2024; 14:273. [PMID: 38254442 PMCID: PMC10812798 DOI: 10.3390/ani14020273] [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: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.
Collapse
Affiliation(s)
- Mengfei Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dan Yue
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
- Faculty of Animal Science and Technology, Yuxi Agricultural Vocational and Technical College, Yuxi 653106, China
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| |
Collapse
|
5
|
Wan L, Huang Q, Li C, Yu H, Tan G, Wei S, El-Sappah AH, Sooranna S, Zhang K, Pan L, Zhang Z, Lei M. Integrated metabolome and transcriptome analysis identifies candidate genes involved in triterpenoid saponin biosynthesis in leaves of Centella asiatica (L.) Urban. FRONTIERS IN PLANT SCIENCE 2024; 14:1295186. [PMID: 38283979 PMCID: PMC10811118 DOI: 10.3389/fpls.2023.1295186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024]
Abstract
Centella asiatica (L.) Urban is a well-known medicinal plant which has multiple pharmacological properties. Notably, the leaves of C. asiatica contain large amounts of triterpenoid saponins. However, there have only been a few studies systematically elucidating the metabolic dynamics and transcriptional differences regarding triterpenoid saponin biosynthesis during the leaf development stages of C. asiatica. Here, we performed a comprehensive analysis of the metabolome and transcriptome to reveal the dynamic patterns of triterpenoid saponin accumulation and identified the key candidate genes associated with their biosynthesis in C. asiatica leaves. In this study, we found that the key precursors in the synthesis of terpenoids, including DMAPP, IPP and β-amyrin, as well as 22 triterpenes and eight triterpenoid saponins were considered as differentially accumulated metabolites. The concentrations of DMAPP, IPP and β-amyrin showed significant increases during the entire stage of leaf development. The levels of 12 triterpenes decreased only during the later stages of leaf development, but five triterpenoid saponins rapidly accumulated at the early stages, and later decreased to a constant level. Furthermore, 48 genes involved in the MVA, MEP and 2, 3-oxidosqualene biosynthetic pathways were selected following gene annotation. Then, 17 CYP450s and 26 UGTs, which are respectively responsible for backbone modifications, were used for phylogenetic-tree construction and time-specific expression analysis. From these data, by integrating metabolomics and transcriptomics analyses, we identified CaHDR1 and CaIDI2 as the candidate genes associated with DMAPP and IPP synthesis, respectively, and CaβAS1 as the one regulating β-amyrin synthesis. Two genes from the CYP716 family were confirmed as CaCYP716A83 and CaCYP716C11. We also selected two UGT73 families as candidate genes, associated with glycosylation of the terpenoid backbone at C-3 in C. asiatica. These findings will pave the way for further research on the molecular mechanisms associated with triterpenoid saponin biosynthesis in C. asiatica.
Collapse
Affiliation(s)
- Lingyun Wan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Haixia Yu
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guiyu Tan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Shugen Wei
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Suren Sooranna
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Kun Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| |
Collapse
|
6
|
Wei Z, Fang Y, Shi W, Chu Z, Zhao B. Transcriptional Modulation Reveals Physiological Responses to Temperature Adaptation in Acrossocheilus fasciatus. Int J Mol Sci 2023; 24:11622. [PMID: 37511383 PMCID: PMC10380296 DOI: 10.3390/ijms241411622] [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: 06/12/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
In order to explore the molecular regulatory mechanism of temperature acclimation under long-term temperature stress in Acrossocheilus fasciatus, this study used high-throughput sequencing technology to analyze 60 days of breeding under five temperature conditions (12 °C, 16 °C, 20 °C, 24 °C, 28 °C). Compared with 20 °C, 9202, 4959 differentially expressed genes (DEGs) were discovered in low-temperature groups (12 °C, 16 °C), whereas 133 and 878 DEGs were discovered in high-temperature groups (24 °C, 28 °C), respectively. The KEGG functional enrichment analysis revealed that DEGs were primarily enriched in tight junction, PI3 K-Akt signaling pathway and protein digestion and absorption in low-temperature groups, and mainly enriched in proximal tubule bicarbonate reclamation, protein digestion and absorption, and HIF-1 signaling pathway in high-temperature groups. The viability of transcriptome sequencing-based screening of DEGs for temperature adaptation in A. fasciatus was shown by the selection of eight DEGs for further validation by quantitative real-time PCR (qRT-PCR), the findings of which were consistent with the RNA-seq data. According to the findings, protein digestion and absorption were primarily regulated by temperature variations, physiological stress was a significant regulator in regulation under high-temperature stress, and the immune system was a significant regulator in regulation under low-temperature stress. The transcriptional patterns of A. fasciatus under temperature stress are revealed in this study. This knowledge is crucial for understanding how A. fasciatus adapts to temperature and can help us better comprehend the environmental difficulties that A. fasciatus adaptation faces.
Collapse
Affiliation(s)
- Zhenzhu Wei
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yi Fang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Wei Shi
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhangjie Chu
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| | - Bo Zhao
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| |
Collapse
|
7
|
Peng X, Khan Z, Liu XM, Deng SL, Fang YG, Zhang M, Su XH, Xing LX, Yan XR. Embryonic Development of Parthenogenetic and Sexual Eggs in Lower Termites. INSECTS 2023; 14:640. [PMID: 37504646 PMCID: PMC10380263 DOI: 10.3390/insects14070640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
Worldwide, termites are one of few social insects. In this research, the stages of embryonic development in the parthenogenetic and sexual eggs of Reticulitermes aculabialis and R. flaviceps were observed and described. In R. flaviceps, the egg development of the FF and FM groups happened during the early phases of development, whereas in R. aculabialis, this appeared mainly during the late phase of development. The variance in the number of micropyles between the R. flaviceps FF colony type and the R. aculabialis FF colony type was statistically significant. Five stages of egg development were found in both types of R. aculabialis but only the sexual eggs of R. flaviceps. In R. flaviceps, 86% of the parthenogenetic eggs stopped growing during the blastoderm development, with the yolk cell assembling frequently in the center of the egg. According to the results of the single-cell transcriptome sequencing, we investigated the egg-to-larval expression level of genes (pka, map2k1, mapk1/3, hgk, mkp, and pax6) and indicated that the levels of essential gene expression in RaFF were considerably higher than in RfFF (p < 0.05). We also discovered that the oocyte cleavage rate in the FF colony type was considerably lower in R. flaviceps compared to R. aculabialis, which gave rise to a smaller number of mature oocytes in R. flaviceps. During ovulation in both species, oocytes underwent activation and one or two cleavage events, but the development of unfertilized eggs ceased in R. flaviceps. It was shown that termite oocyte and embryonic development were heavily influenced by genes with significant expressions. Results from the databases KEGG, COG, and GO unigenes revealed the control of numerous biological processes. This study is the first to complete a database of parthenogenetic and sexual eggs of R. flaviceps and R. aculabialis.
Collapse
Affiliation(s)
- Xin Peng
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
| | - Zahid Khan
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
- Zoology Department, University of Swabi, Swabi 23561, Khyber Pakhtunkhwa, Pakistan
| | - Xiao-Min Liu
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
| | - Shi-Lin Deng
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
| | - Yong-Gang Fang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
| | - Min Zhang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
| | - Xiao-Hong Su
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
- Xi’an Brand of Chinese Academy of Sciences, Xi’an 710043, China
| | - Lian-Xi Xing
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
- Xi’an Brand of Chinese Academy of Sciences, Xi’an 710043, China
| | - Xing-Rong Yan
- College of Life Sciences, Northwest University, Xi’an 710069, China; (X.P.); (Z.K.); (X.-M.L.); (S.-L.D.); (Y.-G.F.); (M.Z.); (X.-H.S.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
- Xi’an Brand of Chinese Academy of Sciences, Xi’an 710043, China
| |
Collapse
|
8
|
Tian S, Liu Q, Qu J, Yang M, Ma Q, Liu J, Shao P, Liu Y. Whole-Transcriptome Analysis on the Leaves of Rosa chinensis Jacq. under Exposure to Polycyclic Aromatic Hydrocarbons. TOXICS 2023; 11:610. [PMID: 37505575 PMCID: PMC10386715 DOI: 10.3390/toxics11070610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
The leaves of plants can be recommended as a cheap and sustainable environmental protection tool to mitigate PAHs with high toxicity in the ambient environment because they can serve as a reactor to remove ambient PAHs. Although previous studies have demonstrated that PAHs exhibit toxicological features, our knowledge about how ambient PAHs influence the leaves of plants is limited regarding the leaves of plants reducing ambient PAHs as a reactor. In this study, 1-year-old Rosa chinensis Jacq. with good growth potential was selected as a model plant. The leaves of Rosa chinensis Jacq. were exposed to 16 types of PAHs in the environmental concentration exposure group (0.1 μg L-1) and high-concentration exposure group (5 μg L-1) for seven days. In comparison, the leaves of Rosa chinensis Jacq. were exposed to de-ionized water and were chosen as the control group. During the exposure periods, the physiological parameters of leaves including, chlorophyll value, water content, temperature and nitrogen, were monitored using a chlorophyll meter. After 7 days of exposure, the leaves in the control and exposure groups were collected and used for whole-transcriptome analysis. Our results demonstrate that significant differentially expressed genes were observed in the leaves of Rosa chinensis Jacq. exposed to individual PAHs at 5 μg L-1 compared to the control group. These differentially expressed genes were involved in seven main pathways using bioinformatic analyses. In contrast, the levels of PAHs at environmentally relevant concentrations had negligible impacts on the physiological parameters and the gene transcription levels of the leaves of Rosa chinensis Jacq. Our results may provide direct evidence to remove ambient PAHs using terrestrial trees without considering the risk of PAHs at environmentally relevant concentrations on the leaves of terrestrial plants.
Collapse
Affiliation(s)
- Shili Tian
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Qingyang Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jingming Qu
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Ming Yang
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Qiaoyun Ma
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Jia Liu
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Peng Shao
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| | - Yanju Liu
- Beijing Center for Physical and Chemical Analysis, Institute of Analysis and Testing, Beijing Academy of Science and Technology, Beijing 100089, China
| |
Collapse
|
9
|
Deng Q, Zhang Y, Liu K, Zheng G, Gao L, Li Z, Huang M, Jiang Y. Transcriptome profiles reveal gene regulation of ginger flowering induced by photoperiod and light quality. BOTANICAL STUDIES 2023; 64:12. [PMID: 37237171 DOI: 10.1186/s40529-023-00388-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Under natural conditions, ginger (Zingiber officinale Rosc.) rarely blossom and has seed, which limits new variety breeding of ginger and industry development. In this study, the effects of different photoperiods and light quality on flowering induction in ginger were performed, followed by gene expression analysis of flower buds differentiation under induced treatment using RNA-seq technology. RESULTS First, both red light and long light condition (18 h light/6 h dark) could effectively induce differentiation of flower buds in ginger. Second, a total of 3395 differentially expressed genes were identified from several different comparisons, among which nine genes, including CDF1, COP1, GHD7, RAV2-like, CO, FT, SOC1, AP1 and LFY, were identified to be associated with flowering in induced flower buds and natural leaf buds. Aside from four down-regulated genes (CDF1, COP1, GHD7 and RAV2-like), other five genes were all up-regulated expression. These differentially expressed genes were mainly classified into 2604 GO categories, which were further enriched into 120 KEGG metabolic pathways. Third, expression change of flowering-related genes in ginger indicated that the induction may negatively regulated expression of CDF1, COP1, GHD7 and RAV2-like, and subsequently positively regulated expression of CO, FT, SOC1, LFY and AP1, which finally led to ginger flowering. In addition, the RNA-seq results were verified by qRT-PCR analysis of 18 randomly selected genes, which further demonstrated the reliability of transcriptome analysis. CONCLUSION This study revealed the ginger flowering mechanism induced by light treatment and provided abundant gene information, which contribute to the development of hybrid breeding of ginger.
Collapse
Affiliation(s)
- Qinyu Deng
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404000, China
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yangtao Zhang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404000, China
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Kang Liu
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Guo Zheng
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404000, China
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Longyan Gao
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhexin Li
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Mengjun Huang
- Research Institute for Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Yusong Jiang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404000, China.
- College of Resources and Environment, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
10
|
Singh R, Singh A, Mahato AK, Paliwal R, Tiwari G, Kumar A. De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata. Int J Mol Sci 2023; 24:ijms24119212. [PMID: 37298166 DOI: 10.3390/ijms24119212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.
Collapse
Affiliation(s)
- Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Ajay Kumar Mahato
- The Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Gunjan Tiwari
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| |
Collapse
|
11
|
March of molecular breeding techniques in the genetic enhancement of herbal medicinal plants: present and future prospects. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00406-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
12
|
Zhang W, Xu X, Li J, Shen Y. Transcriptomic Analysis of the Liver and Brain in Grass Carp (Ctenopharyngodon idella) Under Heat Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:856-870. [PMID: 35930066 DOI: 10.1007/s10126-022-10148-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Temperature is a major environmental factor that influences growth, development, metabolism, and physiological performance in fish. Grass carp (Ctenopharyngodon idella) is a highly productive fish in freshwater culture. To understand the molecular mechanism of grass carp under heat stress, we used RNA-Seq to analyze the liver and brain transcriptome of 12 libraries constructed from high-temperature (36 °C) and control (28 °C) groups. We obtained 42.49 and 42.57 GB of clean data from six liver and six brain libraries, respectively, and identified 2,534 genes that were differentially expressed in liver tissue and 1622 in brain tissue (P < 0.05). According to KEGG analysis, significant differences occurred in the expression of genes involved in metabolic and immune pathways, such as the cAMP signaling pathway, apoptosis, calcium signaling pathway, lipid metabolism, and protein processing in endoplasmic reticulum and peroxisome proliferator-activated receptor signaling pathways. This study revealed that high temperature enhanced lipid metabolism, reduced fatty acid synthesis, and disrupted the immune system of grass carp. These results investigated the molecular regulation of heat stress in grass carp and provided valuable information for the healthy culture of grass carp under high temperatures.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
| |
Collapse
|
13
|
Molecular cloning and characterization of Triterpenoid Biosynthetic Pathway Gene HMGS in Centella asiatica (Linn.). Mol Biol Rep 2022; 49:4555-4563. [DOI: 10.1007/s11033-022-07300-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
|
14
|
Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
Collapse
|
15
|
Ranjith GP, Jisha S, Hemanthakumar AS, Saji CV, Shenoi RA, Sabu KK. Impact of potential stimulants on asiaticoside and madecassoside levels and expression of triterpenoid-related genes in axenic shoot cultures of Centella asiatica (L.) Urb. PHYTOCHEMISTRY 2021; 186:112735. [PMID: 33839454 DOI: 10.1016/j.phytochem.2021.112735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The triterpenoid saponins, asiaticoside and madecassoside from Centella asiatica (L.) Urb. are known to have a wide range of applications in pharmaceutical and cosmetic industries. The effect of addition of Potential Metabolite Stimulants (PMSs) - casein acid hydrolysate, meat peptone, salicylic acid, copper sulphate, and silver nitrate, on the concentrations of these saponins and transcript levels of associated genes encoding important biosynthetic enzymes, was assessed in axenic shoot cultures of C. asiatica. Among the stimulants, silver nitrate induced asiaticoside content approximately 6-fold increase in madecassoside levels, after three weeks post-treatment with a decrease in biomass compared to its control. Gene expression analysis of essential genes involved in triterpenoid synthesis such as β-amyrin synthase showed an upregulation of approximately 50-fold at the third week of silver nitrate treatment compared to control. These findings suggest that silver nitrate can act as a metabolite stimulant, to enhance the formation of triterpenoids in axenic shoot culture of C. asiatica, which could be utilized in studying the regulation of terpenoid biosynthesis and biotechnological application for the increased production of these bioactive molecules.
Collapse
Affiliation(s)
- Gouri Priya Ranjith
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - S Jisha
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - Achutan Sudarsanan Hemanthakumar
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India
| | - Chinthu V Saji
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus, Kottayam, 686009, Kerala, India
| | - Rajesh A Shenoi
- Inter University Centre for Biomedical Research & Super Speciality Hospital, Mahatma Gandhi University Campus, Kottayam, 686009, Kerala, India
| | - Kallevettankuzhy Krishnannair Sabu
- Division of Biotechnology and Bioinformatics, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, 695562, Kerala, India.
| |
Collapse
|
16
|
Pootakham W, Naktang C, Kongkachana W, Sonthirod C, Yoocha T, Sangsrakru D, Jomchai N, U-Thoomporn S, Romyanon K, Toojinda T, Tangphatsornruang S. De novo chromosome-level assembly of the Centella asiatica genome. Genomics 2021; 113:2221-2228. [PMID: 34022344 DOI: 10.1016/j.ygeno.2021.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/05/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
Centella asiatica is a herbaceous, perennial species indigenous to India and Southeast Asia. C. asiatica possesses several medicinal properties: anti-aging, anti-inflammatory, wound healing and memory enhancing. The lack of available genomics resources significantly impedes the improvement of C. asiatica varieties through molecular breeding. Here, we combined the 10× Genomics linked-read technology and the long-range HiC technique to obtain the genome assembly. The final assembly contained nine pseudomolecules, corresponding to the haploid chromosome number in C. asiatica. These nine chromosomes covered 402,536,584 bases or 93.6% of the 430-Mb assembly. Comparative genomics analyses based on single-copy orthologous genes showed that C. asiatica and the common ancestor of Coriandrum sativum (coriander) and Daucus carota (carrot) diverged about 48 million years ago. This assembly provides a valuable reference genome for future molecular studies, varietal development through marker-assisted breeding and comparative genomics studies in C. asiatica.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Kanokwan Romyanon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | |
Collapse
|
17
|
Transcriptome analysis of genes involved in starch biosynthesis in developing Chinese chestnut (Castanea mollissima Blume) seed kernels. Sci Rep 2021; 11:3570. [PMID: 33574357 PMCID: PMC7878784 DOI: 10.1038/s41598-021-82130-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Chinese chestnut (Castanea mollissima Blume) seed kernels (CCSK) with high quality and quantity of starch has emerged as a potential raw material for food industry, but the molecular regulatory mechanism of starch accumulation in developing CCSK is still unclear. In this study, we firstly analyzed the fruit development, starch accumulation, and microscopic observation of dynamic accumulation of starch granules of developing CCSK from 10 days after flowering (DAF) to 100 DAF, of which six representative CCSK samples (50–100 DAF) were selected for transcriptome sequencing analysis. Approximately 40 million valid reads were obtained, with an average length of 124.95 bp, which were searched against a reference genome, returning 38,146 unigenes (mean size = 1164.19 bp). Using the DESeq method, 1968, 1573, 1187, 1274, and 1494 differentially expressed unigenes were identified at 60:50, 70:60, 80:70, 90:80 and 100:90 DAF, respectively. The relationship between the unigene transcriptional profiles and starch dynamic patterns in developing CCSK was comparatively analyzed, and the specific unigenes encoding for metabolic enzymes (SUSY2, PGM, PGI, GPT, NTT, AGP3, AGP2, GBSS1, SS1, SBE1, SBE2.1, SBE2.2, ISA1, ISA2, ISA3, and PHO) were characterized to be involved potentially in the biosynthesis of G-1-P, ADPG, and starch. Finally, the temporal transcript profiles of genes encoding key enzymes (susy2, pgi2, gpt1, agp2, agp3, gbss1, ss1, sbe1, sbe2.1, sbe2.2, isa1, isa2, isa3, and pho) were validated by quantitative real-time PCR (qRT-PCR). Our findings could help to reveal the molecular regulatory mechanism of starch accumulation in developing CCSK and may also provide potential candidate genes for increasing starch content in Chinese chestnut or other starchy crops.
Collapse
|
18
|
Torbati FA, Ramezani M, Dehghan R, Amiri MS, Moghadam AT, Shakour N, Elyasi S, Sahebkar A, Emami SA. Ethnobotany, Phytochemistry and Pharmacological Features of Centella asiatica: A Comprehensive Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1308:451-499. [PMID: 33861456 DOI: 10.1007/978-3-030-64872-5_25] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Centella asiatica (CA) or Gotu cola is an herbal plant from the Apiaceae family with a long history of usage in different traditional medicines. It has long been used for the treatment of various ailments such as central nervous system (CNS), skin and gastrointestinal disorders especially in the Southeast Asia. This chapter focused on the phytochemical constituent and pharmacological activities of CA based on preclinical and clinical studies. Additionally, botanical description and distribution, traditional uses, interactions, and safety issues are reviewed. Electronic databases of Google Scholar, Scopus, PubMed, and Web of Science were searched to obtain relevant studies on the pharmacological activities of CA. Approximately, 124 chemical compounds including triterpenoids, polyphenolic compounds, and essential oils have been isolated and identified from CA. Ethnomedicinal applications of CA mostly include treatment of gastrointestinal diseases, wounds, nervous system disorders, circulatory diseases, skin problems, respiratory ailments, diabetes and sleep disorders in various ethnobotanical practices. Pharmacological studies revealed a wide range of beneficial effects of CA on CNS, cardiovascular, lung, liver, kidney, gastrointestinal, skin, and endocrine system. Among them, neuroprotective activity, wound healing and treatment of venous insufficiency, as well as antidiabetic activity seem to be more frequently reported. At the moment, considering various health benefits of CA, it is marketed as an oral supplement as well as a topical ingredient in some cosmetic products. Additional preclinical studies and particularly randomized controlled trials are needed to clarify the therapeutic roles of CA.
Collapse
Affiliation(s)
- Farshad Abedi Torbati
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahin Ramezani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Dehghan
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Ali Tafazoli Moghadam
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Shakour
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sepideh Elyasi
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland
| | - Seyed Ahmad Emami
- Department of Traditional Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
19
|
Ren Z, Liu J, Din GMU, Zhang H, Du Z, Chen W, Liu T, Zhang J, Zhao S, Gao L. Transcriptome analysis of wheat spikes in response to Tilletia controversa Kühn which cause wheat dwarf bunt. Sci Rep 2020; 10:21567. [PMID: 33299089 PMCID: PMC7725808 DOI: 10.1038/s41598-020-78628-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Wheat dwarf bunt is caused by Tilletia controversa Kühn, which is one of the most destructive diseases of wheat worldwide. To explore the interaction of T. controversa and wheat, we analysed the transcriptome profile of spikes of the susceptible wheat cultivar Dongxuan 3, which was subjected to a T. controversa infection and a mock infection. The results obtained from a differential expression analysis of T. controversa-infected plants compared with mock-infected ones showed that 10,867 out of 21,354 genes were upregulated, while 10,487 genes were downregulated, and these genes were enriched in 205 different pathways. Our findings demonstrated that the genes associated with defence against diseases, such as PR-related genes, WRKY transcription factors and mitogen-activated protein kinase genes, were more highly expressed in response to T. controversa infection. Additionally, a number of genes related to physiological attributes were expressed during infection. Three pathways were differentiated based on the characteristics of gene ontology classification. KEGG enrichment analysis showed that twenty genes were expressed differentially during the infection of wheat with T. controversa. Notable changes were observed in the transcriptomes of wheat plants after infection. The results of this study may help to elucidate the mechanism governing the interactions between this pathogen and wheat plants and may facilitate the development of new methods to increase the resistance level of wheat against T. controversa, including the overexpression of defence-related genes.
Collapse
Affiliation(s)
- Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianjian Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,School of Agriculture, Yangtze University, Hubei, 434025, China
| | - Ghulam Muhae Ud Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Han Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Key Laboratory at Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Shihezi University, Xinjiang, 832003, China
| | - Zhenzhen Du
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianmin Zhang
- School of Agriculture, Yangtze University, Hubei, 434025, China
| | - Sifeng Zhao
- Key Laboratory at Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Shihezi University, Xinjiang, 832003, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
20
|
Alcazar Magana A, Wright K, Vaswani A, Caruso M, Reed RL, Bailey CF, Nguyen T, Gray NE, Soumyanath A, Quinn J, Stevens JF, Maier CS. Integration of mass spectral fingerprinting analysis with precursor ion (MS1) quantification for the characterisation of botanical extracts: application to extracts of Centella asiatica (L.) Urban. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:722-738. [PMID: 32281154 PMCID: PMC7587007 DOI: 10.1002/pca.2936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/12/2020] [Accepted: 03/22/2020] [Indexed: 05/16/2023]
Abstract
INTRODUCTION The phytochemical composition of plant material governs the bioactivity and potential health benefits as well as the outcomes and reproducibility of laboratory studies and clinical trials. OBJECTIVE The objective of this work was to develop an efficient method for the in-depth characterisation of plant extracts and quantification of marker compounds that can be potentially used for subsequent product integrity studies. Centella asiatica (L.) Urb., an Ayurvedic herb with potential applications in enhancing mental health and cognitive function, was used as a case study. METHODS A quadrupole time-of-flight analyser in conjunction with an optimised high-performance liquid chromatography (HPLC) separation was used for in-depth untargeted fingerprinting and post-acquisition precursor ion quantification to determine levels of distinct phytochemicals in various C. asiatica extracts. RESULTS We demonstrate the utility of this workflow for the characterisation of extracts of C. asiatica. This integrated workflow allowed the identification or tentative identification of 117 compounds, chemically interconnected based on Tanimoto chemical similarity, and the accurate quantification of 24 phytochemicals commonly found in C. asiatica extracts. CONCLUSION We report a phytochemical analysis method combining liquid chromatography, high resolution mass spectral data acquisition, and post-acquisition interrogation that allows chemical fingerprints of botanicals to be obtained in conjunction with accurate quantification of distinct phytochemicals. The variability in the composition of specialised metabolites across different C. asiatica accessions was substantial, demonstrating that detailed characterisation of plant extracts is a prerequisite for reproducible use in laboratory studies, clinical trials and safe consumption. The methodological approach is generally applicable to other botanical products.
Collapse
Affiliation(s)
- Armando Alcazar Magana
- Department of ChemistryOregon State UniversityCorvallisORUSA
- Linus Pauling InstituteOregon State UniversityCorvallisORUSA
| | - Kirsten Wright
- Department of NeurologyOregon Health and Science UniversityPortlandORUSA
| | - Ashish Vaswani
- Department of ChemistryOregon State UniversityCorvallisORUSA
| | - Maya Caruso
- Department of NeurologyOregon Health and Science UniversityPortlandORUSA
| | - Ralph L. Reed
- Department of Pharmaceutical SciencesOregon State UniversityCorvallisORUSA
- Linus Pauling InstituteOregon State UniversityCorvallisORUSA
| | | | - Thuan Nguyen
- OHSU‐PSU School of Public Health, Oregon Health & Science UniversityPortlandORUSA
| | - Nora E. Gray
- Department of NeurologyOregon Health and Science UniversityPortlandORUSA
| | - Amala Soumyanath
- Department of NeurologyOregon Health and Science UniversityPortlandORUSA
| | - Joseph Quinn
- Department of NeurologyOregon Health and Science UniversityPortlandORUSA
- Department of Neurology and Parkinson's Disease Research Education and Clinical Care Center (PADRECC), VA Portland Healthcare SystemPortlandORUSA
| | - Jan F. Stevens
- Department of Pharmaceutical SciencesOregon State UniversityCorvallisORUSA
- Linus Pauling InstituteOregon State UniversityCorvallisORUSA
| | - Claudia S. Maier
- Department of ChemistryOregon State UniversityCorvallisORUSA
- Linus Pauling InstituteOregon State UniversityCorvallisORUSA
| |
Collapse
|
21
|
Han L, Li Y, Meng X, Chu G, Guo Y, Noman M, Dong Y, Li H, Yang J, Du L. De novo transcriptome sequencing of Paecilomyces tenuipes revealed genes involved in adenosine biosynthesis. Mol Med Rep 2020; 22:3976-3984. [PMID: 32901833 PMCID: PMC7533470 DOI: 10.3892/mmr.2020.11477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 08/06/2020] [Indexed: 11/06/2022] Open
Abstract
The use of Paecilomyces tenuipes (P. tenuipes), a Chinese medicinal fungus in scientific research, is limited due to its low adenosine content. To improve adenosine production, the present study investigated the gene network of adenosine biosynthesis in P. tenuipes via transcriptome analysis. Mycelia of P. tenuipes cultured for 24 h (PT24), 102 h (PT102) and 196 h (PT192) were subjected to RNA sequencing. In total, 13,353 unigenes were obtained. Based on sequence similarity, 8,099 unigenes were annotated with known proteins. Of these 8,099 unigenes, 5,123 had functions assigned based on Gene Ontology terms while 4,158 were annotated based on the Eukaryotic Orthologous Groups database. Moreover, 1,272 unigenes were mapped to 281 Kyoto Encyclopedia of Genes and Genomes pathways. In addition, the differential gene expression of the three libraries was also performed. A total of 601, 1,658 and 628 differentially expressed genes (DEGs) were detected in PT24 vs. PT102, PT24 vs. PT192 and PT102 vs. PT192 groups, respectively. Reverse transcription‑quantitative PCR was performed to analyze the expression levels of 14 DEGs putatively associated with adenosine biosynthesis in P. tenuipes. The results showed that two DEGs were closely associated with adenosine accumulation of P. tenuipes. The present study not only provides an improved understanding of the genetic information of P. tenuipes but also the findings can be used to aid research into P. tenuipes.
Collapse
Affiliation(s)
- Long Han
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Yaying Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Xinyu Meng
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Guodong Chu
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Yongxin Guo
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Muhammad Noman
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Yuanyuan Dong
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Haiyan Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Jing Yang
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| | - Linna Du
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, School of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, P.R. China
| |
Collapse
|
22
|
Comparative transcriptome analysis to identify putative genes related to trichome development in Ocimum species. Mol Biol Rep 2020; 47:6587-6598. [PMID: 32860161 DOI: 10.1007/s11033-020-05710-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Genus Ocimum is known to have species possessing important therapeutic essential oil. The major phytoconstituents of essential oil in Ocimum species are phenylpropanoids and terpenoids. The essential oil is accumulated in the trichomes; the specialized structures predominantly found on leaves and other tissues. The development of trichome is integrated with development of plant and leaf and also tightly coordinated with the primary and secondary metabolic pathways producing essential oil constituents. In continuation to our studies on elucidating/understanding the mechanism of biosynthesis of essential oil pathways in Ocimum species, we have performed comparative transcriptome analysis to investigate the role of trichome-related gene expression in the regulation of biosynthetic pathways of essential oil. The essential oil biogenesis is tightly integrated with primary metabolic activities, the analysis for the expression pattern of genes related to primary metabolism and its relationship with secondary metabolism was evaluated in comparative manner. Physiological parameters in relation to primary metabolism such as photosynthetic pigment content, soluble sugar content, and invertase enzymes along with morphological parameters were analysed in O. basilicum and O. sanctum. Differential expression profiling uncovered about 8116 and 2810 differentially expressed transcripts in O. basilicum and O. sanctum, respectively. Enrichment of differentially expressed genes were analysed in relation to metabolic pathways, primary metabolism and secondary metabolism. Trichome related genes identified from the Ocimum species vis-à-vis their expression profiles suggested higher expression in O. basilicum. The findings in this study provide interesting insights into the role of trichome-related transcripts in relation to essential oil content in Ocimum species. The study is valuable as this is the first study on revealing the transcripts and their role in trichome development and essential oil biogenesis in two major species of Ocimum.
Collapse
|
23
|
Srivastava G, Garg A, Misra RC, Chanotiya CS, Ghosh S. Transcriptome analysis and functional characterization of oxidosqualene cyclases of the arjuna triterpene saponin pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110382. [PMID: 32005387 DOI: 10.1016/j.plantsci.2019.110382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/25/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Arjuna (Terminalia arjuna) tree has been popular in Indian traditional medicine to treat cardiovascular ailments. The tree accumulates bioactive triterpene glycosides (saponins) and aglycones (sapogenins), in a tissue-preferential manner. Oleanane triterpenes/saponins (derived from β-amyrin) with potential cardioprotective function predominantly accumulate in the bark. However, arjuna triterpene saponin pathway enzymes remain to be identified and biochemically characterized. Here, we employed a combined transcriptomics, metabolomics and biochemical approach to functionally define a suite of oxidosqualene cyclases (OSCs) that catalyzed key reactions towards triterpene scaffold diversification. De novo assembly of 131 millions Illumina NextSeq500 sequencing reads obtained from leaf and stem bark samples led to a total of 156,650 reference transcripts. Four distinct OSCs (TaOSC1-4) with 54-71 % sequence identities were identified and functionally characterized. TaOSC1, TaOSC3 and TaOSC4 were biochemically characterized as β-amyrin synthase, cycloartenol synthase and lupeol synthase, respectively. However, TaOSC2 was found to be a multifunctional OSC producing both α-amyrin and β-amyrin, but showed a preference for α-amyrin product. Both TaOSC1 and TaOSC2 produced β-amyrin, the direct precursor for oleanane triterpene/saponin biosynthesis; but, TaOSC1 transcript expressed preferentially in bark, suggesting a major role of TaOSC1 in the biosynthesis of oleanane triterpenes/saponins in bark.
Collapse
Affiliation(s)
- Gaurav Srivastava
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Chemical Sciences Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
| |
Collapse
|
24
|
Tripathi S, Sangwan RS, Mishra B, Jadaun JS, Sangwan NS. Berry transcriptome: insights into a novel resource to understand development dependent secondary metabolism in Withania somnifera (Ashwagandha). PHYSIOLOGIA PLANTARUM 2020; 168:148-173. [PMID: 30767228 DOI: 10.1111/ppl.12943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 01/31/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
Withania somnifera (Ashwagandha) is considered as Rasayana in Indian systems of medicine. This study reports a novel transcriptome of W. somnifera berries, with high depth, quality and coverage. Assembled and annotated transcripts for nearly all genes related with the withanolide biosynthetic pathway were obtained. Tissue-wide gene expression analysis reflected almost similar definitions for the terpenoid pathway in leaf, root and berry tissues with relatively higher abundance of transcripts linked to steroid, phenylpropanoid metabolism as well as flavonoid metabolism in berries. The metabolome map generated from the data embodied transcripts from 143 metabolic pathways connected together and mediated collectively by about 1792 unique enzyme functions specific to berry, leaf and root tissues, respectively. Transcripts specific to cytochrome p450 (CYP450), methyltransferases and glycosyltransferases were distinctively located in a tissue specific manner and exhibited a complex network. Significant distribution of transcription factor genes such as MYB, early light inducible protein (ELI), minichromosome maintenance1, agamous, deficiens and serum response factor (MADS) and WRKY etc. was observed, as the major transcriptional regulators of secondary metabolism. Validation of the assembly was ascertained by cloning WsELI, which has a light dependent regulatory role in development. Quantitative expression of WsELI was observed to be considerably modulated upon exposure to abiotic stress and elicitors. Co-relation of over-expression of WsELI, may provide new aspects for the functional role of ELI proteins in plants linked to secondary metabolism. The study offers the first comprehensive and comparative evaluation of W. somnifera transcriptome data between the three tissues and across other members of Solanaceae (Nicotiana, Solanum and Capsicum) with respect to major pathways and their metabolome regulation.
Collapse
Affiliation(s)
- Sandhya Tripathi
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by Act of Parliament), Ghaziabad 201002, Uttar Pradesh, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by Act of Parliament), Ghaziabad 201002, Uttar Pradesh, India
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), Mohali 140306, Punjab, India
| | - Bhawana Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by Act of Parliament), Ghaziabad 201002, Uttar Pradesh, India
| | - Jyoti Singh Jadaun
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), Mohali 140306, Punjab, India
| | - Neelam Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by Act of Parliament), Ghaziabad 201002, Uttar Pradesh, India
- Department of Biochemistry, School of Interdisciplinary and Applied Life Sciences, Central University of Haryana, Mahendergarh 123031, Haryana, India
| |
Collapse
|
25
|
Szeliga M, Ciura J, Grzesik M, Tyrka M. Identification of candidate genes involved in steroidal alkaloids biosynthesis in organ-specific transcriptomes of Veratrum nigrum L. Gene 2019; 712:143962. [PMID: 31288057 DOI: 10.1016/j.gene.2019.143962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/10/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
Veratrum nigrum is protected plant of Melanthiaceae family, able to synthetize unique steroidal alkaloids important for pharmacy. Transcriptomes from leaves, stems and rhizomes of in vitro maintained V. nigrum plants were sequenced and annotated for genes and markers discovery. Sequencing of samples derived from the different organs resulted in a total of 108,511 contigs with a mean length of 596 bp. Transcripts derived from leaf and stalk were annotated at 28%, and 38% in Nr nucleotide database, respectively. The sequencing revealed 949 unigenes related with lipid metabolism, including 73 transcripts involved in steroids and genus-specific steroid alkaloids biosynthesis. Additionally, 3203 candidate SSRs markers we identified in unigenes with average density of one SSR locus every 6.2 kb sequence. Unraveling of biochemical machinery of the pathway responsible for steroidal alkaloids will open possibility to design and optimize biotechnological process. The transcriptomic data provide valuable resources for biochemical, molecular genetics, comparative transcriptomics, functional genomics, ecological and evolutionary studies of V. nigrum.
Collapse
Affiliation(s)
- Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland.
| | - Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland; Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Michalina Grzesik
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland; Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Ćwiklińskiej 1, 35-601 Rzeszów, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, Powstańców Warszawy 6 Ave, 35-595 Rzeszów, Poland
| |
Collapse
|
26
|
Gao Y, Zhao M, Wu XH, Li D, Borthakur D, Ye JH, Zheng XQ, Lu JL. Analysis of Differentially Expressed Genes in Tissues of Camellia sinensis during Dedifferentiation and Root Redifferentiation. Sci Rep 2019; 9:2935. [PMID: 30814540 PMCID: PMC6393419 DOI: 10.1038/s41598-019-39264-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/21/2019] [Indexed: 12/04/2022] Open
Abstract
Tissue culture is very important for identifying the gene function of Camellia sinensis (L.) and exploiting novel germplasm through transgenic technology. Regeneration system of tea plant has been explored but not been well established since the molecular mechanism of tea plant regeneration is not clear yet. In this study, transcriptomic analysis was performed in the initial explants of tea plant and their dedifferentiated and redifferentiated tissues. A total of 93,607 unigenes were obtained through de novo assembly, and 7,193 differentially expressed genes (DEGs) were screened out from the 42,417 annotated unigenes. Much more DEGs were observed during phase transition rather than at growth stages of callus. Our KOG and KEGG analysis, and qPCR results confirmed that phase transition of tea plant was closely related to the mechanism that regulate expression of genes encoding the auxin- and cytokinin-responsive proteins, transcription factor MYB15 and ethylene-responsive transcription factor ERF RAP2-12. These findings provide a reliable foundation for elucidating the mechanism of the phase transition and may help to optimize the regeneration system by regulating the gene expression pattern.
Collapse
Affiliation(s)
- Ying Gao
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Min Zhao
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Xiao-Han Wu
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Da Li
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | | | - Jian-Hui Ye
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Xin-Qiang Zheng
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China
| | - Jian-Liang Lu
- Zhejiang University Tea Research Institute, Hangzhou, 310058, P.R. China.
| |
Collapse
|
27
|
Yang S, Sun X, Jiang X, Wang L, Tian J, Li L, Zhao M, Zhong Q. Characterization of the Tibet plateau Jerusalem artichoke ( Helianthus tuberosus L.) transcriptome by de novo assembly to discover genes associated with fructan synthesis and SSR analysis. Hereditas 2019; 156:9. [PMID: 30774580 PMCID: PMC6364414 DOI: 10.1186/s41065-019-0086-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/27/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers and represent the foundation for their formation, processing and utilization of yield; and are also widely used in new sugar-based materials, bioenergy processing, ecological management, and functional feed. To identify key genes in the metabolic pathway of fructans in Jerusalem artichoke, high-throughput sequencing was performed using Illumina Hi Seq™ 2500 equipment to construct a transcriptome library. RESULTS Qinghai-Tibet Plateau Jerusalem artichoke "Qingyu No.1" was used as the material; roots, stems, leaves, flowers and tubers of Jerusalem artichoke in its flowering stage were mixed into a mosaic of the Jerusalem artichoke transcriptome library, obtaining 63,089 unigenes with an average length of 713.6 bp. Gene annotation through the Nr, Swiss Prot, GO, KOG and KEGG databases revealed 34.95 and 46.91% of these unigenes had similar sequences in the Nr and Swiss Prot databases. The GO classification showed the Jerusalem artichoke unigenes were divided into three ontologies, with a total of 49 functional groups encompassing biological processes, cellular components, and molecular functions. Among them, there were more unigenes involved in the functional groups for cellular processes, metabolic processes, and single-organism processes. 38,999 unigenes were annotated by KOG and divided into 25 categories according to their functions; the most common annotation being general function prediction. A total of 13,878 unigenes (22%) were annotated in the KEGG database, with the largest proportion corresponding to pathways related to carbohydrate metabolism. A total of 12 unigenes were involved in the synthesis and degradation of fructan. Cluster analysis revealed the candidate 12 unigene proteins were dispersed in the 5 major families of proteins involved in fructan synthesis and degradation. The synergistic effect of INV gene is necessary during fructose synthesis and degradation in Jerusalem artichoke tuber development. The sequencing data from the transcriptome of this species can provide a reliable data basis for the identification and assessment of the expression of the members of the INV gene family.A simple sequence repeat (SSR) loci search was performed on the transcriptome data of Jerusalem artichoke, identifying 6635 eligible SSR loci with a large proportion of dinucleotide and trinucleotide repeats, and the most different motifs were repeated 5 times and 6 times. Dinucleotide and trinucleotide repeat motifs were the most frequent, with AG/CT and ACC/GGT repeat motifs accounting for the highest proportion. CONCLUSIONS In this study, a database search of the transcriptome of the Jerusalem artichoke from the Qinghai Tibet Plateau was conducted by high throughput sequencing technology to obtain important transcriptional and SSR loci information. This allowed characterization of the overall expression features of the Jerusalem artichoke transcriptome, identifying the key genes involved in metabolism in this species. In turn, this offers a foundation for further research on the regulatory mechanisms of fructan metabolism in Jerusalem artichoke.
Collapse
Affiliation(s)
- Shipeng Yang
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Xuemei Sun
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Xiaoting Jiang
- Qinghai Higher Vocational & Technical College Institute, Ledu, 810799 China
| | - Lihui Wang
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Jie Tian
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Li Li
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Mengliang Zhao
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Qiwen Zhong
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| |
Collapse
|
28
|
Malik S. The Phytochemical Composition, Biological Effects and Biotechnological Approaches to the Production of High-Value Essential Oil from Geranium. ESSENTIAL OIL RESEARCH 2019. [PMCID: PMC7122831 DOI: 10.1007/978-3-030-16546-8_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Geraniaceae family plants are highly reputed aromatic and medicinal perennial branched herbs. The high economic value of these plants is due to their secondary metabolites, especially essential oil of foliage, which is a complex mixture of volatile phytochemicals, such as terpenes, esters, aldehydes, alcohols, ketones and phenols. The main phytoconstituents of the essential oil belong to the terpenoid group of metabolites, such as monoterpenes, sesquiterpenes, diterpenes and their esters. Of these, geraniol, linalool, citronellol and their esters (50–70%) generally constitute a major portion of essential oil, responsible for its fragrance. Essential oil is biosynthesized in specialized tissues known as glandular trichomes present in leaves, green branches and fresh flowers. Geraniaceae family plants have been highly useful in the perfumery, cosmetics, aromatherapy, pharmaceuticals and food industries. Several pharmacological properties such as antifungal, anti-inflammatory, anti-cancerous, anti-depressant, antibacterial, antioxidant, antiseptic, anti-dysentery, and antidiabetic properties are attributed to the presence of geranium oil. Further, it improves blood circulation, treats congestion, cleans the lymphatic system, strengthens the immune system, and is effective in combating nervousness, constipation, insomnia, anxiety and high blood pressure. The chapter discusses the phytochemical composition, pharmacological properties, genomics of essential oil biosynthetic pathway, enhancement of essential oil yield, and several biotechnological approaches to enhance the quantity as well as quality of essential oil in geranium.
Collapse
Affiliation(s)
- Sonia Malik
- ARC Centre of Excellence in Plant Energy Biology and School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia, Graduate Program in Health Sciences, Biological and Health Sciences Center, Federal University of Maranhão, São Luís, Maranhão Brazil
| |
Collapse
|
29
|
Choudhri P, Rani M, Sangwan RS, Kumar R, Kumar A, Chhokar V. De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism. BMC Genomics 2018; 19:427. [PMID: 29859051 PMCID: PMC5984767 DOI: 10.1186/s12864-018-4819-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aloe vera is a perennial, succulent, drought-resistant plant that exhibits many pharmacological characteristics such as wound healing ability against skin burns, anti-ulcer, anti-inflammatory, anti-tumor, anti-viral, anti-hypercholesterolemic, anti-hyperglycemic, anti-asthmatic and much more. Despite great medicinal worth, little genomic information is available on Aloe vera. This study is an initiative to explore the full-scale functional genomics of Aloe vera by generating whole transcriptome sequence database, using Illumina HiSeq technology and its progressive annotation specifically with respect to the metabolic specificity of the plant. RESULTS Transcriptome sequencing of root and leaf tissue of Aloe vera was performed using Illumina paired-end sequencing technology. De novo assembly of high quality paired-end reads, resulted into 1,61,733 and 2,21,792 transcripts with mean length of 709 and 714 nucleotides for root and leaf respectively. The non-redundant transcripts were clustered using CD-HIT-EST, yielding a total of 1,13,063 and 1,41,310 unigenes for root and leaf respectively. A total of 6114 and 6527 CDS for root and leaf tissue were enriched into 24 different biological pathway categories using KEGG pathway database. DGE profile prepared by calculating FPKM values was analyzed for differential expression of specific gene encoding enzymes involved in secondary metabolite biosynthesis. Sixteen putative genes related to saponin, lignin, anthraquinone, and carotenoid biosynthesis were selected for quantitative expression by real-time PCR. DGE as well as qRT PCR expression analysis represented up-regulation of secondary metabolic genes in root as compared to leaf. Furthermore maximum number of genes was found to be up-regulated after the induction of methyl jasmonate, which stipulates the association of secondary metabolite synthesis with the plant's defense mechanism during stress. Various transcription factors including bHLH, NAC, MYB were identified by searching predicted CDS against PlantTFdb. CONCLUSIONS This is the first transcriptome database of Aloe vera and can be potentially utilized to characterize the genes involved in the biosynthesis of important secondary metabolites, metabolic regulation, signal transduction mechanism, understanding function of a particular gene in the biology and physiology of plant of this species as well as other species of Aloe genus.
Collapse
Affiliation(s)
- Pragati Choudhri
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| | - Muniya Rani
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| | - Rajender S. Sangwan
- Centre of Innovative and Applied Bioprocessing (CIAB), (A National Institute under Department of Biotechnology, Govt. of India), Sector-81 (Knowledge City), Manauli P.O., S.A.S. Nagar, Mohali, Punjab 140306 India
| | - Ravinder Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| | - Anil Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| | - Vinod Chhokar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| |
Collapse
|
30
|
Gray NE, Alcazar Magana A, Lak P, Wright KM, Quinn J, Stevens JF, Maier CS, Soumyanath A. Centella asiatica - Phytochemistry and mechanisms of neuroprotection and cognitive enhancement. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:161-194. [PMID: 31736679 PMCID: PMC6857646 DOI: 10.1007/s11101-017-9528-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/17/2017] [Indexed: 05/18/2023]
Abstract
This review describes in detail the phytochemistry and neurological effects of the medicinal herb Centella asiatica (L.) Urban. C. asiatica is a small perennial plant that grows in moist, tropical and sub-tropical regions throughout the world. Phytochemicals identified from C. asiatica to date include isoprenoids (sesquiterpenes, plant sterols, pentacyclic triterpenoids and saponins) and phenylpropanoid derivatives (eugenol derivatives, caffeoylquinic acids, and flavonoids). Contemporary methods for fingerprinting and characterization of compounds in C. asiatica extracts include liquid chromatography and/or ion mobility spectrometry in conjunction with high-resolution mass spectrometry. Multiple studies in rodent models, and a limited number of human studies support C. asiatica's traditional reputation as a cognitive enhancer, as well as its anxiolytic and anticonvulsant effects. Neuroprotective effects of C.asiatica are seen in several in vitro models, for example against beta amyloid toxicity, and appear to be associated with increased mitochondrial activity, improved antioxidant status, and/or inhibition of the pro-inflammatory enzyme, phospholipase A2. Neurotropic effects of C. asiatica include increased dendritic arborization and synaptogenesis, and may be due to modulations of signal transduction pathways such as ERK1/2 and Akt. Many of these neurotropic and neuroprotective properties of C.asiatica have been associated with the triterpene compounds asiatic acid, asiaticoside and madecassoside. More recently, caffeoylquinic acids are emerging as a second important group of active compounds in C. asiatica, with the potential of enhancing the Nrf2-antioxidant response pathway. The absorption, distribution, metabolism and excretion of the triterpenes, caffeoylquinic acids and flavonoids found in C. asiatica have been studied in humans and animal models, and the compounds or their metabolites found in the brain. This review highlights the remarkable potential for C. asiatica extracts and derivatives to be used in the treatment of neurological conditions, and considers the further research needed to actualize this possibility.
Collapse
Affiliation(s)
- Nora E. Gray
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | | | - Parnian Lak
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
| | - Kirsten M. Wright
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| | - Joseph Quinn
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
- Department of Neurology and Parkinson’s Disease Research Education and Clinical Care Center (PADRECC),
Portland Veterans Affairs Medical Center, Portland, OR, USA 97239
| | - Jan F. Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97331
| | - Claudia S. Maier
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97331
| | - Amala Soumyanath
- Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239
| |
Collapse
|
31
|
Kim OT, Jin ML, Lee DY, Jetter R. Characterization of the Asiatic Acid Glucosyltransferase, UGT73AH1, Involved in Asiaticoside Biosynthesis in Centella asiatica (L.) Urban. Int J Mol Sci 2017; 18:E2630. [PMID: 29210992 PMCID: PMC5751233 DOI: 10.3390/ijms18122630] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 01/27/2023] Open
Abstract
Centella asiatica (L.) Urban contains two ursane-type triterpene saponins, asiaticoside and madecassoside, as major secondary metabolites. In order to select candidate genes encoding UDP-glucosyltransferases (UGTs) involved in asiaticoside biosynthesis, we performed transcriptomic analysis of leaves elicited by methyl jasmonate (MeJA). Among the unigenes, 120 isotigs and 13 singletons of unique sequences were annotated as UGTs, including 37 putative full-length cDNAs, and 15 of the putative UGT genes were named according to the UGT committee nomenclature protocols. One of them, UGT73AH1, was characterized by heterologous expression in Escherichia coli BL21 (DE3) cells. After induction with IPTG, a total protein extract was assayed with UDP-glucose and asiatic acid. UPLC-QTOF/MS analysis showed that UGT73AH1 catalyzes the glycosylation of asiatic acid to its monoglucoside. It remains unclear whether glycosylation occurs on the triterpene C-2α, C-3β, C-23, or C-28 position. However, it is very likely that UGT73AH1 glucosylates the C-28 position, because only C-28 bears a glucose moiety in the final pathway product of asiatic acid, while C-2α, C-3β, and C-23 remain un-conjugated.
Collapse
Affiliation(s)
- Ok Tae Kim
- Department of Herbal Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea.
| | - Mei Lan Jin
- Department of Herbal Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea.
| | - Dae Young Lee
- Department of Herbal Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 27709, Korea.
| | - Reinhard Jetter
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
| |
Collapse
|
32
|
Tripathi S, Sangwan RS, Narnoliya LK, Srivastava Y, Mishra B, Sangwan NS. Transcription factor repertoire in Ashwagandha (Withania somnifera) through analytics of transcriptomic resources: Insights into regulation of development and withanolide metabolism. Sci Rep 2017; 7:16649. [PMID: 29192149 PMCID: PMC5709440 DOI: 10.1038/s41598-017-14657-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/03/2017] [Indexed: 11/17/2022] Open
Abstract
Transcription factors (TFs) are important regulators of cellular and metabolic functions including secondary metabolism. Deep and intensive RNA-seq analysis of Withania somnifera using transcriptomic databases provided 3532 annotated transcripts of transcription factors in leaf and root tissues, belonging to 90 different families with major abundance for WD-repeat (174 and 165 transcripts) and WRKY (93 and 80 transcripts) in root and leaf tissues respectively, followed by that of MYB, BHLH and AP2-ERF. Their detailed comparative analysis with Arabidopsis thaliana, Capsicum annum, Nicotiana tabacum and Solanum lycopersicum counterparts together gave interesting patterns. However, no homologs for WsWDR representatives, LWD1 and WUSCHEL, were observed in other Solanaceae species. The data extracted from the sequence read archives (SRA) in public domain databases were subjected to re-annotation, re-mining, re-analysis and validation for dominant occurrence of WRKY and WD-repeat (WDR) gene families. Expression of recombinant LWD1 and WUSCHEL proteins in homologous system led to enhancements in withanolide content indicating their regulatory role in planta in the biosynthesis. Contrasting expression profiles of WsLWD1 and WsWUSCHEL provided tissue-specific insights for their participation in the regulation of developmental processes. The in-depth analysis provided first full-spectrum and comparative characteristics of TF-transcripts across plant species, in the perspective of integrated tissue-specific regulation of metabolic processes including specialized metabolism.
Collapse
Affiliation(s)
- Sandhya Tripathi
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by an Act of Parliament),, AcSIR Campus, CSIR-HRDC, Sector-19, Kamla Nehru Nagar, Ghaziabad, Ghaziabad, 201002, Uttar Pradesh, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, 140306, Punjab, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by an Act of Parliament),, AcSIR Campus, CSIR-HRDC, Sector-19, Kamla Nehru Nagar, Ghaziabad, Ghaziabad, 201002, Uttar Pradesh, India
| | - Lokesh Kumar Narnoliya
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Yashdeep Srivastava
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Bhawana Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by an Act of Parliament),, AcSIR Campus, CSIR-HRDC, Sector-19, Kamla Nehru Nagar, Ghaziabad, Ghaziabad, 201002, Uttar Pradesh, India
| | - Neelam Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR) (An Institution of National Importance by an Act of Parliament),, AcSIR Campus, CSIR-HRDC, Sector-19, Kamla Nehru Nagar, Ghaziabad, Ghaziabad, 201002, Uttar Pradesh, India.
| |
Collapse
|
33
|
Zhu H, Liu J, Wen Q, Chen M, Wang B, Zhang Q, Xue Z. De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits. PLoS One 2017; 12:e0187117. [PMID: 29145430 PMCID: PMC5690621 DOI: 10.1371/journal.pone.0187117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/13/2017] [Indexed: 11/19/2022] Open
Abstract
Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1-6 h). Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism.
Collapse
Affiliation(s)
- Haisheng Zhu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Jianting Liu
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qingfang Wen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Mindong Chen
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Bin Wang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Qianrong Zhang
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| | - Zhuzheng Xue
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Vegetable Research Center, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Engineering Research Center for Vegetables, Fuzhou, Fujian, China
| |
Collapse
|
34
|
de Costa F, Barber CJS, Kim YB, Reed DW, Zhang H, Fett-Neto AG, Covello PS. Molecular cloning of an ester-forming triterpenoid: UDP-glucose 28-O-glucosyltransferase involved in saponin biosynthesis from the medicinal plant Centella asiatica. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:9-17. [PMID: 28716424 DOI: 10.1016/j.plantsci.2017.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/12/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
Triterpene saponins include bioactive compounds with structures consisting of triterpene aglycones (sapogenins) and one or more sugar moieties linked through acetal or ester glycosidic linkages at one or more sites. Centella asiatica (L.) Urban is a medicinal plant that contains bioactive ursane-type saponins, such as madecassoside and asiaticoside. In this work, glucosylation of triterpenoids in C. asiatica was investigated starting with plant extracts. An enzyme capable of glucosylating asiatic and madecassic acids was partially purified. Proteomics methods and cDNA sequence data were employed as tools to obtain a full-length cDNA clone encoding a glucosyltransferase. The recombinant gene product, UGT73AD1, was functionally expressed in Escherichia coli and purified by immobilized metal-affinity chromatography. Purified recombinant UGT73AD1 was found to have a narrow specificity, glucosylating asiatic and madecassic acids at the C28 carboxyl. mRNA accumulated in all tissues tested (leaves, stems, roots and flowers), with highest expression in leaves. Thus, UGT73AD1 was identified as a triterpenoid carboxylic acid: UDP-glucose 28-O-glucosyltransferase that appears to be involved in saponin biosynthesis in C. asiatica.
Collapse
Affiliation(s)
- Fernanda de Costa
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada; Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil.
| | - Carla J S Barber
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada.
| | - Yeon-Bok Kim
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada; Herbal Crop Research Division, Department of Herbal Crop Research, Bisanro 92, Eumseong, Chungbuk, 369-873, Korea.
| | - Darwin W Reed
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada.
| | - Haixia Zhang
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada.
| | - Arthur G Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil.
| | - Patrick S Covello
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada.
| |
Collapse
|
35
|
Ciura J, Szeliga M, Grzesik M, Tyrka M. Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum). PLANTA 2017; 245:977-991. [PMID: 28161815 PMCID: PMC5393294 DOI: 10.1007/s00425-017-2657-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/30/2017] [Indexed: 05/21/2023]
Abstract
Representational difference analysis of cDNA was performed and differential products were sequenced and annotated. Candidate genes involved in biosynthesis of diosgenin in fenugreek were identified. Detailed mechanism of diosgenin synthesis was proposed. Fenugreek (Trigonella foenum-graecum L.) is a valuable medicinal and crop plant. It belongs to Fabaceae family and has a unique potential to synthesize valuable steroidal saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were used to enhance the content of sterols and steroidal sapogenins in in vitro grown plants for representational difference analysis of cDNA (cDNA-RDA). To identify candidate genes involved in diosgenin biosynthesis, differential, factor-specific libraries were subject to the next-generation sequencing. Approximately 9.9 million reads were obtained, trimmed, and assembled into 31,491 unigenes with an average length of 291 bp. Then, functional annotation and gene ontogeny enrichment analysis was performed by aligning all-unigenes with public databases. Within the transcripts related to sterol and steroidal saponin biosynthesis, we discovered novel candidate genes of diosgenin biosynthesis and validated their expression using quantitative RT-PCR analysis. Based on these findings, we supported the idea that diosgenin is biosynthesized from cycloartenol via cholesterol. This is the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes enriched in low copy sequences contributed substantially to our understanding of the biochemical pathways of steroid synthesis in fenugreek.
Collapse
Affiliation(s)
- Joanna Ciura
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Magdalena Szeliga
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Michalina Grzesik
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszow University of Technology, al. Powstańców Warszawy 6, 35-959, Rzeszów, Poland.
| |
Collapse
|
36
|
Jadaun JS, Sangwan NS, Narnoliya LK, Singh N, Bansal S, Mishra B, Sangwan RS. Over-expression of DXS gene enhances terpenoidal secondary metabolite accumulation in rose-scented geranium and Withania somnifera: active involvement of plastid isoprenogenic pathway in their biosynthesis. PHYSIOLOGIA PLANTARUM 2017; 159:381-400. [PMID: 27580641 DOI: 10.1111/ppl.12507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 05/08/2023]
Abstract
Rose-scented geranium (Pelargonium spp.) is one of the most important aromatic plants and is well known for its diverse perfumery uses. Its economic importance is due to presence of fragrance rich essential oil in its foliage. The essential oil is a mixture of various volatile phytochemicals which are mainly terpenes (isoprenoids) in nature. In this study, on the geranium foliage genes related to isoprenoid biosynthesis (DXS, DXR and HMGR) were isolated, cloned and confirmed by sequencing. Further, the first gene of 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway, 1-deoxy-d-xylulose-5-phosphate synthase (GrDXS), was made full length by using rapid amplification of cDNA ends strategy. GrDXS contained a 2157 bp open reading frame that encoded a polypeptide of 792 amino acids having calculated molecular weight 77.5 kDa. This study is first report on heterologous expression and kinetic characterization of any gene from this economically important plant. Expression analysis of these genes was performed in different tissues as well as at different developmental stages of leaves. In response to external elicitors, such as methyl jasmonate, salicylic acid, light and wounding, all the three genes showed differential expression profiles. Further GrDXS was over expressed in the homologous (rose-scented geranium) as well as in heterologous (Withania somnifera) plant systems through genetic transformation approach. The over-expression of GrDXS led to enhanced secondary metabolites production (i.e. essential oil in rose-scented geranium and withanolides in W. somnifera). To the best of our knowledge, this is the first report showing the expression profile of the three genes related to isoprenoid biosynthesis pathways operated in rose-scented geranium as well as functional characterization study of any gene from rose-scented geranium through a genetic transformation system.
Collapse
Affiliation(s)
- Jyoti Singh Jadaun
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neelam S Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Lokesh K Narnoliya
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Neha Singh
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Shilpi Bansal
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Bhawana Mishra
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
- Center of Innovative and Applied Bioprocessing (A National Institute under Department of Biotechnology, Govt. of India), C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali - 160071, Punjab, India
| |
Collapse
|
37
|
Narnoliya LK, Kaushal G, Singh SP, Sangwan RS. De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis. BMC Genomics 2017; 18:74. [PMID: 28086783 PMCID: PMC5234130 DOI: 10.1186/s12864-016-3437-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/19/2016] [Indexed: 01/11/2023] Open
Abstract
Background Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain. Therefore, to begin the gains in molecular understanding of specialized metabolic pathways of the plant, de novo sequencing of rose-scented geranium leaf transcriptome, transcript assembly, annotation, expression profiling as well as their validation were carried out. Results De novo transcriptome analysis resulted a total of 78,943 unique contigs (average length: 623 bp, and N50 length: 752 bp) from 15.44 million high quality raw reads. In silico functional annotation led to the identification of several putative genes representing terpene, ascorbic acid and tartaric acid biosynthetic pathways, hormone metabolism, and transcription factors. Additionally, a total of 6,040 simple sequence repeat (SSR) motifs were identified in 6.8% of the expressed transcripts. The highest frequency of SSR was of tri-nucleotides (50%). Further, transcriptome assembly was validated for randomly selected putative genes by standard PCR-based approach. In silico expression profile of assembled contigs were validated by real-time PCR analysis of selected transcripts. Conclusion Being the first report on transcriptome analysis of rose-scented geranium the data sets and the leads and directions reflected in this investigation will serve as a foundation for pursuing and understanding molecular aspects of its biology, and specialized metabolic pathways, metabolic engineering, genetic diversity as well as molecular breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3437-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lokesh K Narnoliya
- Center of Innovative and Applied Bioprocessing (A National Institute under the Department of Biotechnology, Govt. of India), S.A.S. Nagar, Mohali, Punjab, India
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing (A National Institute under the Department of Biotechnology, Govt. of India), S.A.S. Nagar, Mohali, Punjab, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (A National Institute under the Department of Biotechnology, Govt. of India), S.A.S. Nagar, Mohali, Punjab, India.
| | - Rajender S Sangwan
- Center of Innovative and Applied Bioprocessing (A National Institute under the Department of Biotechnology, Govt. of India), S.A.S. Nagar, Mohali, Punjab, India.
| |
Collapse
|
38
|
Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis. Int J Genomics 2016; 2016:7840914. [PMID: 28097124 PMCID: PMC5206855 DOI: 10.1155/2016/7840914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/29/2016] [Accepted: 11/07/2016] [Indexed: 01/13/2023] Open
Abstract
G. pentaphyllum (Gynostemma pentaphyllum), a creeping herbaceous perennial with many important medicinal properties, is widely distributed in Asia. Gypenosides (triterpenoid saponins), the main effective components of G. pentaphyllum, are well studied. FPS (farnesyl pyrophosphate synthase), SS (squalene synthase), and SE (squalene epoxidase) are the main enzymes involved in the synthesis of triterpenoid saponins. Considering the important medicinal functions of G. pentaphyllum, it is necessary to investigate the transcriptomic information of G. pentaphyllum to facilitate future studies of transcriptional regulation. After sequencing G. pentaphyllum, we obtained 50,654,708 unigenes. Next, we used RPKM (reads per kilobases per million reads) to calculate expression of the unigenes and we performed comparison of our data to that contained in five common databases to annotate different aspects of the unigenes. Finally, we noticed that FPS, SS, and SE showed differential expression of enzymes in DESeq. Leaves showed the highest expression of FPS, SS, and SE relative to the other two tissues. Our research provides transcriptomic information of G. pentaphyllum in its natural environment and we found consistency in unigene expression, enzymes expression (FPS, SS, and SE), and the distribution of gypenosides content in G. pentaphyllum. Our results will enable future related studies of G. pentaphyllum.
Collapse
|
39
|
de Costa F, Barber CJS, Reed DW, Covello PS. From Plant Extract to a cDNA Encoding a Glucosyltransferase Candidate: Proteomics and Transcriptomics as Tools to Help Elucidate Saponin Biosynthesis in Centella asiatica. Methods Mol Biol 2016; 1405:43-8. [PMID: 26843164 DOI: 10.1007/978-1-4939-3393-8_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Centella asiatica (L.) Urban (Apiaceae), a small annual plant that grows in India, Sri Lanka, Malaysia, and other parts of Asia, is well-known as a medicinal herb with a long history of therapeutic uses. The bioactive compounds present in C. asiatica leaves include ursane-type triterpene sapogenins and saponins-asiatic acid, madecassic acid, asiaticoside, and madecassoside. Various bioactivities have been shown for these compounds, although most of the steps in the biosynthesis of triterpene saponins, including glycosylation, remain uncharacterized at the molecular level. This chapter describes an approach that integrates partial enzyme purification, proteomics methods, and transcriptomics, with the aim of reducing the number of cDNA candidates encoding for a glucosyltransferase involved in saponin biosynthesis and facilitating the elucidation of the pathway in this medicinal plant.
Collapse
Affiliation(s)
- Fernanda de Costa
- Plant Physiology Laboratory, Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Porto Alegre, RS, 91501-970, Brazil.,Center for Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carla J S Barber
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK, Canada, S7N 0W9
| | - Darwin W Reed
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK, Canada, S7N 0W9
| | - Patrick S Covello
- National Research Council of Canada, 110 Gymnasium Pl., Saskatoon, SK, Canada, S7N 0W9.
| |
Collapse
|
40
|
Li J, Zhen W, Long D, Ding L, Gong A, Xiao C, Jiang W, Liu X, Zhou T, Huang L. De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome. PLoS One 2016; 11:e0164235. [PMID: 27764127 PMCID: PMC5072632 DOI: 10.1371/journal.pone.0164235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/21/2016] [Indexed: 01/09/2023] Open
Abstract
Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P. heterophylla. We obtained 616,413,316 clean reads that we assembled into 127, 334 unique sequences with an N50 length of 951 bp. Among these unigenes, 53,184 unigenes (41.76%) were annotated in a public database and 39, 795 unigenes were assigned to 356 KEGG pathways; 23,714 unigenes (8.82%) had high homology with the genes from Beta vulgaris. We discovered 32, 095 DEGs in different tissues and performed GO and KEGG enrichment analysis. The most enriched KEGG pathway of secondary metabolism showed up-regulated expression in tuberous roots as compared with the ground parts of P. heterophylla. Moreover, we identified 72 candidate genes involved in triterpenoids saponins biosynthesis in P. heterophylla. The expression profiles of 11 candidate unigenes were analyzed by quantitative real-time PCR (RT-qPCR). Our study established a global transcriptome database of P. heterophylla for gene identification and regulation. We also identified the candidate unigenes involved in triterpenoids saponins biosynthesis. Our results provide an invaluable resource for the secondary metabolites and physiological processes in different tissues of P. heterophylla.
Collapse
Affiliation(s)
- Jun Li
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Wei Zhen
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Dengkai Long
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Ling Ding
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Anhui Gong
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Chenghong Xiao
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Weike Jiang
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Xiaoqing Liu
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Tao Zhou
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China
| |
Collapse
|
41
|
Azerad R. Chemical structures, production and enzymatic transformations of sapogenins and saponins from Centella asiatica (L.) Urban. Fitoterapia 2016; 114:168-187. [DOI: 10.1016/j.fitote.2016.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022]
|
42
|
Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
Collapse
Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
| |
Collapse
|
43
|
Feng Y, Zhang L, Fu J, Li F, Wang L, Tan X, Mo W, Cao H. Characterization of Glycolytic Pathway Genes Using RNA-Seq in Developing Kernels of Eucommia ulmoides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3712-3731. [PMID: 27074598 DOI: 10.1021/acs.jafc.5b05918] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Eucommia ulmoides Oliver, the only member of the Eucommiaceae family, is a rare and valuable tree used to produce a highly valued traditional Chinese medicine and contains α-linolenic acid (ALA) up to 60% of the total fatty acids in the kernels (embryos). Glycolysis provides both cellular energy and the intermediates for other biosynthetic processes. However, nothing was known about the molecular basis of the glycolytic pathway in E. ulmoides kernels. The purposes of this study were to identify novel genes of E. ulmoides related to glycolytic metabolism and to analyze the expression patterns of selected genes in the kernels. Transcriptome sequencing based on the Illumina platform generated 96,469 unigenes in four cDNA libraries constructed using RNAs from 70 and 160 days after flowering kernels of both low- and high-ALA varieties. We identified and characterized the digital expression of 120 unigenes coding for 24 protein families involved in kernel glycolytic pathway. The expression levels of glycolytic genes were generally higher in younger kernels than in more mature kernels. Importantly, several unigenes from kernels of the high-ALA variety were expressed more than those from the low-ALA variety. The expression of 10 unigenes encoding key enzymes in the glycolytic pathway was validated by qPCR using RNAs from six kernel stages of each variety. The qPCR data were well consistent with their digital expression in transcriptomic analyses. This study identified a comprehensive set of genes for glycolytic metabolism and suggests that several glycolytic genes may play key roles in ALA accumulation in the kernels of E. ulmoides.
Collapse
Affiliation(s)
- Yanzhi Feng
- Paulownia Research and Development Center, State Forestry Administration , Zhengzhou, Henan 450003, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology , Changsha, Hunan 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology , Changsha, Hunan 410004, China
| | - Jianmin Fu
- Paulownia Research and Development Center, State Forestry Administration , Zhengzhou, Henan 450003, China
| | - Fangdong Li
- Paulownia Research and Development Center, State Forestry Administration , Zhengzhou, Henan 450003, China
| | - Lu Wang
- Paulownia Research and Development Center, State Forestry Administration , Zhengzhou, Henan 450003, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology , Changsha, Hunan 410004, China
| | - Wenjuan Mo
- Forestry Experiment Center of North China, Chinese Academy of Forestry , Beijing 102300, China
| | - Heping Cao
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture , New Orleans, Louisiana 70124, United States
| |
Collapse
|
44
|
Singh AK, Dubey SK. Current trends in Bt crops and their fate on associated microbial community dynamics: a review. PROTOPLASMA 2016; 253:663-681. [PMID: 26560114 DOI: 10.1007/s00709-015-0903-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
Cry protein expressing insect-resistant trait is mostly deployed to control major devastating pests and minimize reliance on the conventional pesticides. However, the ethical and environmental issues are the major constraints in their acceptance, and consequently, the cultivation of genetically modified (GM) crops has invited intense debate. Since root exudates of Bacillus thuringiensis (Bt) crops harbor the insecticidal protein, there is a growing concern about the release and accumulation of soil-adsorbed Cry proteins and their impact on non-target microorganisms and soil microbial processes. This review pertains to reports from the laboratory studies and field trials to assess the Bt toxin proteins in soil microbes and the processes determining the soil quality in conjunction with the existing hypothesis and molecular approaches to elucidate the risk posed by the GM crops. Ecological perturbations hinder the risk aspect of soil microbiota in response to GM crops. Therefore, extensive research based on in vivo and interpretation of results using high-throughput techniques such as NGS on risk assessment are imperative to evaluate the impact of Bt crops to resolve the controversy related to their commercialization. But more studies are needed on the risk associated with stacked traits. Such studies would strengthen our knowledge about the plant-microbe interactions.
Collapse
Affiliation(s)
| | - Suresh Kumar Dubey
- Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
| |
Collapse
|
45
|
Chen C, Li A. Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant. Front Physiol 2016; 7:100. [PMID: 27047386 PMCID: PMC4796566 DOI: 10.3389/fphys.2016.00100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/02/2016] [Indexed: 12/17/2022] Open
Abstract
The rhizome of Fagopyrum dibotrys is a traditional Chinese medicine that has recently gained attention due to substantial findings regarding its bioactive proanthocyanidin (PA) compounds. However, the molecular mechanism underlying PA accumulation in F. dibotrys remains elusive. We previously obtained an irradiation-induced mutant (RM_R) of F. dibotrys that had a higher PA content compared to that of the wild-type (CK_R). The present study aimed to elucidate the molecular mechanism underlying PA accumulation in F. dibotrys by comparing the rhizome transcriptomes of the irradiation-induced mutant and wild-type using RNA-seq analysis. A total of 53,540 unigenes were obtained, of which 29,901 (55.84%) were annotated based on BLAST searches against public databases, and 501 unique sequences were differentially expressed between the two samples, which consisted of 204 up-regulated and 297 down-regulated unigenes. Further analysis showed that the expression patterns of some unigenes encoding enzymes involved in PAs biosynthesis in F. dibotrys rhizomes differed between RM_R and CK_R. In addition, we identified transcription factor families and several cytochrome P450s that may be involved in PA regulation in F. dibotrys. Finally, 12 unigenes that encode PA biosynthetic enzymes were confirmed by qRT-PCR analysis. This study sheds light on the molecular mechanism underlying radiation-mediated flavonoid accumulation and regulation in F. dibotrys rhizomes. These results will also provide a platform for further functional genomic research on this particular species.
Collapse
Affiliation(s)
| | - Ailian Li
- The Cultivation Center, Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| |
Collapse
|
46
|
Ahmed S, Zhan C, Yang Y, Wang X, Yang T, Zhao Z, Zhang Q, Li X, Hu X. The Transcript Profile of a Traditional Chinese Medicine, Atractylodes lancea, Revealing Its Sesquiterpenoid Biosynthesis of the Major Active Components. PLoS One 2016; 11:e0151975. [PMID: 26990438 PMCID: PMC4798728 DOI: 10.1371/journal.pone.0151975] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
Atractylodes lancea (Thunb.) DC., named “Cangzhu” in China, which belongs to the Asteraceae family. In some countries of Southeast Asia (China, Thailand, Korea, Japan etc.) its rhizome, commonly called rhizoma atractylodis, is used to treat many diseases as it contains a variety of sesquiterpenoids and other components of medicinal importance. Despite its medicinal value, the information of the sesquiterpenoid biosynthesis is largely unknown. In this study, we investigated the transcriptome analysis of different tissues of non-model plant A. lancea by using short read sequencing technology (Illumina). We found 62,352 high quality unigenes with an average sequence length of 913 bp in the transcripts of A. Lancea. Among these, 43,049 (69.04%), 30,264 (48.53%), 26,233 (42.07%), 17,881 (28.67%) and 29,057(46.60%) unigenes showed significant similarity (E-value<1e-5) to known proteins in Nr, KEGG, SWISS-PROT, GO, and COG databases, respectively. Of the total 62,352 unigenes, 43,049 (Nr Database) open reading frames were predicted. On the basis of different bioinformatics tools we identify all the enzymes that take part in the terpenoid biosynthesis as well as five different known sesquiterpenoids via cytosolic mevalonic acid (MVA) pathway and plastidal methylerythritol phosphate (MEP) pathways. In our study, 6, 864 Simple Sequence Repeats (SSRs) were also found as great potential markers in A. lancea. This transcriptomic resource of A. lancea provides a great contribution in advancement of research for this specific medicinal plant and more specifically for the gene mining of different classes of terpenoids and other chemical compounds that have medicinal as well as economic importance.
Collapse
Affiliation(s)
- Shakeel Ahmed
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Chuansong Zhan
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yanyan Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuekui Wang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Tewu Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zeying Zhao
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qiyun Zhang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaohua Li
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuebo Hu
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- * E-mail:
| |
Collapse
|
47
|
Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus. Sci Rep 2016; 6:21026. [PMID: 26877149 PMCID: PMC4753472 DOI: 10.1038/srep21026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
Advances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.
Collapse
|
48
|
Cherukupalli N, Divate M, Mittapelli SR, Khareedu VR, Vudem DR. De novo Assembly of Leaf Transcriptome in the Medicinal Plant Andrographis paniculata. FRONTIERS IN PLANT SCIENCE 2016; 7:1203. [PMID: 27582746 PMCID: PMC4987368 DOI: 10.3389/fpls.2016.01203] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/28/2016] [Indexed: 05/05/2023]
Abstract
Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeq™ 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant non-redundant protein database, gene ontology, and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts-using kyoto encyclopedia of genes and genomes database-revealed 5606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs) in 23,168 transcripts. Assembled sequences of transcriptome of A. paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analysis besides identification of key enzymes involved in the various pathways of secondary metabolism.
Collapse
|
49
|
Srivastava S, Sangwan RS, Tripathi S, Mishra B, Narnoliya LK, Misra LN, Sangwan NS. Light and auxin responsive cytochrome P450s from Withania somnifera Dunal: cloning, expression and molecular modelling of two pairs of homologue genes with differential regulation. PROTOPLASMA 2015; 252:1421-37. [PMID: 25687294 DOI: 10.1007/s00709-015-0766-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 01/20/2015] [Indexed: 05/16/2023]
Abstract
Cytochrome P450s (CYPs) catalyse a wide variety of oxygenation/hydroxylation reactions that facilitate diverse metabolic functions in plants. Specific CYP families are essential for the biosynthesis of species-specialized metabolites. Therefore, we investigated the role of different CYPs related to secondary metabolism in Withania somnifera, a medicinally important plant of the Indian subcontinent. In this study, complete complementary DNAs (cDNAs) of four different CYP genes were isolated and christened as WSCYP93Id, WSCYP93Sm, WSCYP734B and WSCYP734R. These cDNAs encoded polypeptides comprising of 498, 496, 522 and 550 amino acid residues with their deduced molecular mass of 56.7, 56.9, 59.4 and 62.2 kDa, respectively. Phylogenetic study and molecular modelling analysis of the four cloned WSCYPs revealed their categorization into two CYP families (CYP83B1 and CYP734A1) belonging to CYP71 and CYP72 clans, respectively. BLASTp searches showed similarity of 75 and 56 %, respectively, between the two CYP members of CYP83B1 and CYP734A1 with major variances exhibited in their N-terminal regions. The two pairs of homologues exhibited differential expression profiles in the leaf tissues of selected chemotypes of W. somnifera as well as in response to treatments such as methyl jasmonate, wounding, light and auxin. Light and auxin regulated two pairs of WSCYP homologues in a developing seedling in an interesting differential manner. Their lesser resemblance and homology with other CYP sequences suggested these genes to be more specialized and distinct ones. The results on chemotype-specific expression patterns of the four genes strongly suggested their key/specialized involvement of the CYPs in the biosynthesis of chemotype-specific metabolites, though their further biochemical characterization would reveal the specificity in more detail. It is revealed that WSCYP93Id and WSCYP93Sm may be broadly involved in the oxygenation reactions in the plant and, thereby, control various pathways involving such metabolic reactions in the plant. As a representative experimental validation of this notion, WSCYP93Id was heterologouly expressed in Escherichia coli and catalytic capabilities of the recombinant WSCYP93Id protein were evaluated using withanolides as substrates. Optimized assays with some major withanolides (withanone, withaferin A and withanolide A) involving spectrophotometric as well as high-pressure liquid chromatography (HPLC)-based evaluation (product detection) of the reactions showed conversion of withaferin A to a hydroxylated product. The genes belonging to other CYP group are possibly involved in some specialised synthesis such as that of brassinosteroids.
Collapse
MESH Headings
- Biotransformation
- Cloning, Molecular
- Computational Biology
- Cytochrome P-450 Enzyme System/chemistry
- Cytochrome P-450 Enzyme System/genetics
- Cytochrome P-450 Enzyme System/metabolism
- Databases, Genetic
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Hydroxylation
- Indoleacetic Acids/pharmacology
- Isoenzymes
- Light
- Models, Molecular
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Medicinal
- Protein Conformation
- Recombinant Proteins/metabolism
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Structure-Activity Relationship
- Substrate Specificity
- Withania/drug effects
- Withania/enzymology
- Withania/genetics
- Withania/radiation effects
- Withanolides/metabolism
Collapse
Affiliation(s)
- Sudhakar Srivastava
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India
- Jacob Blaustein Institute for Desert Research, Albert Katz Department of Dryland Biotechnologies, Ben-Gurion University of the Negev, Negev, Israel
| | - Rajender Singh Sangwan
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India.
- Centre of Innovative and Applied Bioprocessing (CIAB), (A National Institute under Department of Biotechnology, Government of India), Mohali, 1600 71, Punjab, India.
| | - Sandhya Tripathi
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India
| | - Bhawana Mishra
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India
| | - L K Narnoliya
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India
| | - L N Misra
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India
| | - Neelam S Sangwan
- Metabolic and Structural Biology Department, CSIR-Central Institute for Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, UP, India.
- Centre of Innovative and Applied Bioprocessing (CIAB), (A National Institute under Department of Biotechnology, Government of India), Mohali, 1600 71, Punjab, India.
| |
Collapse
|
50
|
Muriira NG, Xu W, Muchugi A, Xu J, Liu A. De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). BMC Genomics 2015; 16:723. [PMID: 26395839 PMCID: PMC4580217 DOI: 10.1186/s12864-015-1908-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Sodom apple (Calotropis gigantea), a member of the Asclepiadaceae family, is a large evergreen shrub native to continental Asia and northern Africa. As an important medicinal shrub and a fiber resource plant, there is an urgent need for developing molecular markers to facilitate breeding and genetic improvement of varieties. Results In this study, using the Illumina high throughput sequencing technique we obtained about 45 million paired end sequencing reads, De novo assembled and generated a total of 133,634 transcripts with a mean of 1837.47 bp in length. Based on protein homology searches against available databases, a total of 21,851 unigenes were functionally annotated. In particular, many transcripts that encode for putative proteins involved in fiber and secondary metabolite biosynthesis were identified and analyzed. Key fiber genes identified were validated experimentally through Real-Time PCR technique. Various transcription factors involved in regulating plant response to abiotic stress were also identified. In addition, based on the unigene sequences assembled, 11,623 microsatellites loci were detected, which provide very useful resources for developing microsatellite molecular markers. Conclusion This study is the first report on transcriptome information in the Calotropis species and provides rich gene transcript resources for conducting further studies on understanding the molecular basis of fiber and secondary metabolite biosynthesis, serving the genetic improvement and resource utilization in Calotropis plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1908-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nkatha G Muriira
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China. .,World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Wei Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Alice Muchugi
- World Agroforestry Centre (ICRAF), P.O. Box 30677-00100, Nairobi, Kenya.
| | - Jianchu Xu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China. .,World Agroforestry Centre, East and Central Asia Office, 132 Lanhei Road, Kunming, 650201, China.
| | - Aizhong Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, Heilongtan, Kunming, 650201, Yunnan, China.
| |
Collapse
|