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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [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: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Goyal P, Devi R, Verma B, Hussain S, Arora P, Tabassum R, Gupta S. WRKY transcription factors: evolution, regulation, and functional diversity in plants. PROTOPLASMA 2023; 260:331-348. [PMID: 35829836 DOI: 10.1007/s00709-022-01794-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.
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Affiliation(s)
- Pooja Goyal
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Ritu Devi
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhawana Verma
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rubeena Tabassum
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suphla Gupta
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Faculty, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Łuczaj Ł, Wolanin M, Drobnik J, Kujawska M, Dumanowski J, Walker K, Tomczyk M. Dysphania schraderiana (Schult.) Mosyakin & Clemants - An overlooked medicinal and ritual plant used in Poland. JOURNAL OF ETHNOPHARMACOLOGY 2022; 284:114755. [PMID: 34673224 DOI: 10.1016/j.jep.2021.114755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The paper discusses the traditional ritual, medicinal and insect repellent use of Dysphania schraderiana in Poland, a plant with little ethnobotanical and phytochemical data. Our research suggests that its properties should be further studied comparing it with the related D. botrys and D. ambrosioides. AIM OF THE WORK D. schraderiana is an aromatic and medicinal annual herb related to D. ambrosioides and D. botrys and practically absent from historical accounts of plant uses in Europe. The aim of this work is to characterise the current use of D. schraderiana in south east Poland on the background of historical Dysphania species use in Europe. MATERIALS AND METHODS The data on D. schraderiana was collected in 2020, based on interviews with 42 people in rural areas of south-eastern Poland where the species is used today. A range of textual sources were searched including old medicinal herbals, pharmaceutical handbooks, ethnobotanical publications and culinary databases regarding all the uses of Dysphania species in Europe. RESULTS In the study area D. schraderiana occurs in the whole spectrum of cultivation stages - from being intentionally cultivated to completely wild. The plant is used mainly as an apotropaic and insect repellent, blessed during Catholic church holidays (mainly Assumption Day), and sometimes used as incense in churches (and blessed on Epiphany Day). D. schraderiana rarely occurs in European historical sources, except sometimes classed as a false, inferior form of D. botrys, which has been known for centuries as a moth repellent and treatment for respiratory illness. We hypothesise that the plant was not easily distinguished from D. botrys and their uses strongly overlapped. For some unknown reason the use of D. botrys died out, whereas a relatively large semi-feral population of D. schraderiana exists in south-eastern Poland where it has remained a culturally important plant. CONCLUSIONS D. schraderiana is a rare case of a non-native plant traditionally used within an area of Europe but previously nearly overlooked in European ethnobotanical literature. Historical uses of Dysphania spp. in other areas of Poland and former Poland (now western Ukraine) suggest that the genus was used more widely in regions beyond the one studied. However, a very compact distribution of use suggests that D. schraderiana may have been brought to SE Poland from a single source outside the study area. Its common name, and use as a holy incense plant, is associated it with the well-known biblical tree resin obtained from Commiphora myrrha (Nees) Engl.
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Affiliation(s)
- Łukasz Łuczaj
- Institute of Biology and Biotechnology, Rzeszów University, Ul. Pigonia 1, 35-310, Rzeszów, Poland.
| | - Mateusz Wolanin
- Institute of Biology and Biotechnology, Rzeszów University, Ul. Pigonia 1, 35-310, Rzeszów, Poland
| | - Jacek Drobnik
- Department of Pharmaceutical Botany and Herbal Medicine, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Ul. Ostrogórska 30, 41-210, Sosnowiec, Poland
| | - Monika Kujawska
- University of Łódź, Institute of Ethnology and Cultural Anthropology, Ul. Lindleya 3/5, 90-131, Łódź, Poland
| | - Jarosław Dumanowski
- Faculty of History, Nicolaus Copernicus University in Toruń, Ul. Bojarskiego 1, 87-100, Toruń, Poland
| | - Kim Walker
- Royal Holloway University, Egham Hill, Egham, TW20 0EX, United Kingdom; Royal Botanic Gardens Kew, The Herbarium, Richmond, TW9 3AE, United Kingdom
| | - Michał Tomczyk
- Department of Pharmacognosy, Faculty of Pharmacy, Medical University of Białystok, Ul. Mickiewicza 2a, 15-230, Białystok, Poland
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Tomescu MS, Sooklal SA, Ntsowe T, Naicker P, Darnhofer B, Archer R, Stoychev S, Swanevelder D, Birner-Grünberger R, Rumbold K. Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PLoS One 2021; 16:e0253741. [PMID: 34283859 PMCID: PMC8291589 DOI: 10.1371/journal.pone.0253741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 06/11/2021] [Indexed: 11/19/2022] Open
Abstract
The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.
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Affiliation(s)
- Mihai-Silviu Tomescu
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Selisha Ann Sooklal
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, UNISA, Johannesburg, South Africa
| | - Thuto Ntsowe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Previn Naicker
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Barbara Darnhofer
- ACIB GmbH, Graz, Austria
- Institute for Pathology, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed, Graz, Austria
| | - Robert Archer
- National Herbarium, South African National Biodiversity Institute, Pretoria, South Africa
| | - Stoyan Stoychev
- Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Dirk Swanevelder
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Ruth Birner-Grünberger
- ACIB GmbH, Graz, Austria
- Institute for Pathology, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed, Graz, Austria
| | - Karl Rumbold
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
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Wang Z, Ma H, Zhang M, Wang Z, Tian Y, Li W, Wang Y. Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions. BMC Genomics 2021; 22:16. [PMID: 33407099 PMCID: PMC7788892 DOI: 10.1186/s12864-020-07266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatile oil having more than 82 identified components of which methyleugenol, safrole, myristicin, and toluene account for about 70% of the total volume. As a sciophyte plant, the amount of light it absorbs through leaves is an important factor for growth and metabolism. RESULTS We grew Asarum plants under full, 50, 28, and 12% sunlight conditions to investigate the effect of different light irradiances on the four major volatile oil components. We employed de novo transcriptome sequencing to understand the transcriptional behavior of Asarum leaves regarding the biosynthetic pathways of the four volatile oil components, photosynthesis and biomass accumulation, and hormone signaling. Our results demonstrated that the increasing light conditions promoted higher percent of the four components. Under full sunlight conditions, cinnamyl alcohol dehydrogenase and cytochrome p450719As were upregulated and led the increased methyleugenol, safrole, and myristicin. The transcriptomic data also showed that Asarum leaves, under full sunlight conditions, adjust their photosynthesis-antenna proteins as a photoprotective response with the help of carotenoids. Plant hormone-signaling related genes were also differentially expressed between full sunlight and low light conditions. CONCLUSIONS High light induces accumulation of major bioactive ingredients A. heterotropides volatile oil and this is ascribed to upregulation of key genes such as cinnamyl alcohol dehydrogenase and cytochrome p450719As. The transcriptome data presented here lays the foundation of further understanding of light responses in sciophytes and provides guidance for increasing bioactive molecules in Asarum.
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Affiliation(s)
- Zhiqing Wang
- Laboratory of Cultivation and Breeding of Medicinal Plants, National Administration of Traditional Chinese Medicine, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Haiqin Ma
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, Jilin, China
| | - Min Zhang
- Laboratory of Cultivation and Breeding of Medicinal Plants, National Administration of Traditional Chinese Medicine, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Ziqing Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, Jilin, China
| | - Yixin Tian
- Laboratory of Cultivation and Breeding of Medicinal Plants, National Administration of Traditional Chinese Medicine, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Wei Li
- State & Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Yingping Wang
- State & Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, Jilin, China
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Niu J, Zhao G, Mi Z, Chen L, Liu S, Wang S, Wang D, Wang Z. De novo sequencing of Bletilla striata (Orchidaceae) transcriptome and identification of genes involved in polysaccharide biosynthesis. Genet Mol Biol 2020; 43:e20190417. [PMID: 32609279 PMCID: PMC7315133 DOI: 10.1590/1678-4685-gmb-2019-0417] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/16/2020] [Indexed: 11/22/2022] Open
Abstract
Bletilla striata polysaccharide (BSP) is the main component of Bletilla striata, which has important pharmacological and pharmacological effects; however, due to the lack of genetic data, the metabolic pathways of BSP remain unclear. For this study, 11 representative resources of B. striata were analyzed, and the BSP contents of the different samples were significantly different; however, the monosaccharide composition of BSP was glucose and mannose. The representative samples were selected to observe their life history in situ, which were then divided and cultured in a greenhouse. Finally, samples from various organs of different plants were combined for transcriptome sequencing using the Illumina system. Our results summarized the BSP metabolic pathway, and we found that there were eight enzyme genes involved in biosynthesis, but these genes showed tissue specificity. Following qRT-PCR validation and comparative analysis, manA showed the highest expression; however, there were significant differences between the two germplasm resources in which the BSP content was significantly different, while UGP2, GPI, PMM, and GMPP had significant differences between the two samples. In summary, this study lays the foundation for further research into BSP metabolism and other physiological processes at the molecular level.
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Affiliation(s)
- Junfeng Niu
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Guangming Zhao
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Zeyuan Mi
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Lijun Chen
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Shuai Liu
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Shiqiang Wang
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Donghao Wang
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
| | - Zhezhi Wang
- Shaanxi Normal University, College of Life Sciences, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Xi'an, Shaanxi, China
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