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Wen CY, Lian JY, Peng WX, Wang ZF, Yang ZG, Cao HL. Genome assembly of Erythrophleum Fordii, a special "ironwood" tree in China. BMC Genom Data 2023; 24:73. [PMID: 38017381 PMCID: PMC10685560 DOI: 10.1186/s12863-023-01176-9] [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: 10/20/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVES Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly. DATA DESCRIPTION This work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads using E. fordii leaf tissues. The de novo assembly contained 864,825,911 bp in the E. fordii genome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.
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Affiliation(s)
- Chang-Yu Wen
- Guangdong Forestry Survey and Planning Institute, Guangzhou, 510520, China
| | - Ju-Yu Lian
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Wei-Xiong Peng
- Guangdong Forestry Survey and Planning Institute, Guangzhou, 510520, China
| | - Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| | - Zhi-Gang Yang
- Guangdong Forestry Survey and Planning Institute, Guangzhou, 510520, China
| | - Hong-Lin Cao
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
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Ashraf MV, Pant S, Khan MAH, Shah AA, Siddiqui S, Jeridi M, Alhamdi HWS, Ahmad S. Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:881. [PMID: 37375828 DOI: 10.3390/ph16060881] [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: 04/14/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.
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Affiliation(s)
- Mohammad Vikas Ashraf
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Shreekar Pant
- Centre for Biodiversity Studies, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - M A Hannan Khan
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Ali Asghar Shah
- Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Mouna Jeridi
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Shoeb Ahmad
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185 234, India
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Bhalla P, Tripathi Y, Varshney VK. Phytochemistry and biological activity of Skimmia laureola leaf essential oil - a review. JOURNAL OF ESSENTIAL OIL RESEARCH 2021. [DOI: 10.1080/10412905.2021.1895337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Piyush Bhalla
- Chemistry & Bioprospecting Division, Forest Research Institute, Dehradun, India
| | - Y.C. Tripathi
- Chemistry & Bioprospecting Division, Forest Research Institute, Dehradun, India
| | - V. K. Varshney
- Chemistry & Bioprospecting Division, Forest Research Institute, Dehradun, India
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Ahmed MJ, Murtaza G, Mehmood A, Bhatti TM. Silver nanoparticles, green synthesis: characterization, in vitro antioxidant and antimicrobial study. INORG NANO-MET CHEM 2019. [DOI: 10.1080/24701556.2019.1661435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Muhammad Jamil Ahmed
- Department of Botany, University of Azad Jammu and Kashmir (UAJK), Muzaffarabad, Pakistan
| | - Ghulam Murtaza
- Department of Botany, University of Azad Jammu and Kashmir (UAJK), Muzaffarabad, Pakistan
| | - Ansar Mehmood
- Department of Botany, University of Poonch Rawalakot (UPR), Rawalakot, Pakistan
| | - Tariq M. Bhatti
- Department of Chemical and Material Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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Joshi RK, Satyal P, Setzer WN. Himalayan Aromatic Medicinal Plants: A Review of their Ethnopharmacology, Volatile Phytochemistry, and Biological Activities. MEDICINES (BASEL, SWITZERLAND) 2016; 3:E6. [PMID: 28930116 PMCID: PMC5456235 DOI: 10.3390/medicines3010006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 01/28/2016] [Accepted: 02/03/2016] [Indexed: 12/26/2022]
Abstract
Aromatic plants have played key roles in the lives of tribal peoples living in the Himalaya by providing products for both food and medicine. This review presents a summary of aromatic medicinal plants from the Indian Himalaya, Nepal, and Bhutan, focusing on plant species for which volatile compositions have been described. The review summarizes 116 aromatic plant species distributed over 26 families.
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Affiliation(s)
- Rakesh K Joshi
- Department of Education, Government of Uttrakhand, Nainital 263001, India.
| | - Prabodh Satyal
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Wiliam N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Epifano F, Fiorito S, Genovese S, Granica S, Vitalini S, Zidorn C. Phytochemistry of the genus Skimmia (Rutaceae). PHYTOCHEMISTRY 2015; 115:27-43. [PMID: 25745856 DOI: 10.1016/j.phytochem.2015.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 02/09/2015] [Accepted: 02/14/2015] [Indexed: 05/22/2023]
Abstract
The genus Skimmia is a rich source of interesting secondary metabolites, including 20 alkaloids derived from anthranilic acid, 45 coumarins, 21 limonoids, four cholestane derivatives, six pentacyclic triterpenes, six flavonoids, and two unusual fatty acid derivatives. Skimmia is employed in folk medicine e.g. against fever, inflammations, and rheumatism. Skimmia extracts, Skimmia essential oils and pure compounds isolated from Skimmia extracts have been experimentally shown to have various bioactivities such as antioxidant, anti-inflammatory, antimicrobial, and insecticidal. In this review we discuss the exact structures of compounds isolated from members of the genus Skimmia, bioactivities of Skimmia extracts and pure compounds derived from them, and systematic implications of the patterns of occurrence of these compounds. Moreover, research gaps and interesting avenues for future research are discussed briefly.
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Affiliation(s)
- Francesco Epifano
- Dipartimento di Farmacia, Università "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66013 Chieti Scalo, CH, Italy
| | - Serena Fiorito
- Dipartimento di Farmacia, Università "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66013 Chieti Scalo, CH, Italy
| | - Salvatore Genovese
- Dipartimento di Farmacia, Università "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66013 Chieti Scalo, CH, Italy
| | - Sebastian Granica
- Department of Pharmacognosy and Molecular Basis of Phytotherapy, Faculty of Pharmacy, Medical University of Warsaw, ul. Banacha 1, 02-097 Warsaw, Poland; Institut für Pharmazie der Universität Innsbruck, Abteilung Pharmakognosie, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Sara Vitalini
- Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Christian Zidorn
- Institut für Pharmazie der Universität Innsbruck, Abteilung Pharmakognosie, Innrain 80/82, A-6020 Innsbruck, Austria.
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Stappen I, Tabanca N, Ali A, Wedge DE, Wanner J, Kaul VK, Lal B, Jaitak V, Gochev VK, Schmidt E, Jirovetz L. Chemical Composition and Biological Activity of Essential Oils from Wild Growing Aromatic Plant Species of Skimmia laureola and Juniperus macropoda from Western Himalaya. Nat Prod Commun 2015. [DOI: 10.1177/1934578x1501000669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Himalayan region is very rich in a great variety of medicinal plants. In this investigation the essential oils of two selected species are described for their antimicrobial and larvicidal as well as biting deterrent activities. Additionally, the odors are characterized. Analyzed by simultaneous GC-MS and GC-FID, the essential oils’ chemical compositions are given. The main components of Skimmia laureola oil were linalool and linalyl acetate whereas sabinene was found as the main compound for Juniperus macropoda essential oil. Antibacterial testing by agar dilution assay revealed highest activity of S. laureola oil against all tested bacteria, followed by J. macropoda oil. Antifungal activity was evaluated against the strawberry anthracnose causing plant pathogens Colletotrichum acutatum, C. fragariae and C. gloeosporioides. Juniperus macropoda essential oil indicated higher antifungal activity against all three pathogens than S. laureola oil. Both essential oils showed biting deterrent activity above solvent control but low larvicidal activity.
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Affiliation(s)
- Iris Stappen
- Department of Medicinal Chemistry, University of Vienna, Vienna, Austria
| | - Nurhayat Tabanca
- National Center for Natural Products Research, The University of Mississippi, University, MS 38677, USA
| | - Abbas Ali
- National Center for Natural Products Research, The University of Mississippi, University, MS 38677, USA
| | - David E. Wedge
- US Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University of Mississippi, University, MS 38677, USA
| | | | - Vijay K. Kaul
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, H.P., India
| | - Brij Lal
- Biodiversity Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vikas Jaitak
- Centre for Chemical and Pharmaceutical Sciences, Central University of Punjab, Bathinda, India
| | - Velizar K. Gochev
- Department of Biochemistry and Microbiology, “Paisii Hilendarski”- University of Plovdiv, Plovdiv, Bulgaria
| | - Erich Schmidt
- Department of Medicinal Chemistry, University of Vienna, Vienna, Austria
| | - Leopold Jirovetz
- Department of Medicinal Chemistry, University of Vienna, Vienna, Austria
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Chemical composition and biological activities of the essential oil of Skimmia laureola leaves. Molecules 2015; 20:4735-45. [PMID: 25786161 PMCID: PMC6272542 DOI: 10.3390/molecules20034735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 11/16/2022] Open
Abstract
The composition of the essential oil from leaves of Skimmia laureola was determined by GC and GC-MS. Twenty-eight components were identified, accounting for 93.9% of the total oil. The oil is mainly composed of monoterpenes (93.5%), of which monoterpene hydrocarbons and oxygenated monoterpenes represent 11.0% and 82.5%, respectively. Sesquiterpenes constitute only 0.3% of the total oil. Linalyl acetate is the main component (50.5%), with linalool (13.1%), geranyl acetate (8.5%) and cis-p-menth-2-en-1-ol (6.2%) as other principal constituents. The essential oil showed a significant antispasmodic activity, in a dose range of 0.03–10 mg/mL. The essential oil also possesses antibacterial and antifungal activities against some pathogenic strains. The phytotoxic and cytotoxic activities were also assessed.
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