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Wu HY, Wong KL, Law STS, Nong W, Chan KT, Hui JHL, Lin G, Chan WH, Shaw PC. Determination of ITS1 haplotypes of Fritillariae Cirrhosae Bulbus by amplicon sequencing. Chin Med 2024; 19:33. [PMID: 38419104 PMCID: PMC10900738 DOI: 10.1186/s13020-024-00911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Fritillariae Cirrhosae Bulbus is an antitussive and expectorant Chinese medicinal material derived from the dried bulbs of six Fritillaria species. In the 2015 edition of the Chinese Pharmacopoeia, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is the officially listed method for their authenfication. Specifically, the ~ 300-bp ITS1 amplicon of only Fritillariae Cirrhosae Bulbus but not other Fritillaria species can be cleaved into two smaller fragments with restriction enzyme SmaI. Considering repeated reported cases of incomplete digestion of ITS1 amplicon, this study aims to investigate the possibility of heterogeneous ITS1 sequences contained in the Fritillariae Cirrhosae Bulbus. METHODS In this study, ITS1 amplicons of Fritillaria Cirrhosae Bulbus and four other Fritillaria species were sequenced on Illumina platform. We utilised high-throughout amplicon sequencing to determine ITS1 haplotypes and their frequencies in Fritillaria genomes. RESULTS Our results showed that all six botanical sources of Fritillariae Cirrhosae Bulbus indeed possess ITS1 haplotypes with no SmaI restriction site, and the average percentages of ITS1 reads containing SmaI restriction site ranged from 63.60% to 91.81%. CONCLUSION Our findings suggest that the incomplete digestion in PCR-RFLP analysis of Fritillariae Cirrhosae Bulbus is caused by the presence of ITS1 haplotypes without SmaI restriction site due to intragenomic heterogeneity.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ka-Lok Wong
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum Law
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wenyang Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Kwun-Tin Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam Hui
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ge Lin
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wing-Han Chan
- Government Chinese Medicines Testing Institute, Chinese Medicine Regulatory Office, Department of Health, Shatin, N.T., Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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Kong BLH, Nong W, Wong KH, Law STS, So WL, Chan JJS, Zhang J, Lau TWD, Hui JHL, Shaw PC. Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway. Genomics 2022; 114:110366. [PMID: 35413434 DOI: 10.1016/j.ygeno.2022.110366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.
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Affiliation(s)
- Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum Law
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai-Lok So
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Johnson Jor-Shing Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jordan Zhang
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Tai-Wai David Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam Hui
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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