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Principles and strategies for species identification based on analysis of whole-genome
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Yu-tong GAN1, Tian-yi XIN1, 2, Wen-jie XU1, 2, Li-jun HAO1, Gui-hong QI1, Qian LOU1, Jing-yuan SONG1, 2, 3, *
Acta Pharmaceutica Sinica | 2023, 58(8) : 2364 - 2374
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Acta Pharmaceutica Sinica | 2023, 58(8): 2364-2374
Principles and strategies for species identification based on analysis of whole-genome
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Yu-tong GAN1, Tian-yi XIN1, 2, Wen-jie XU1, 2, Li-jun HAO1, Gui-hong QI1, Qian LOU1, Jing-yuan SONG1, 2, 3, *
Affiliations
  • 1. Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
  • 2. Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
  • 3. Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China
Published: 2023-08-12 doi: 10.16438/j.0513-4870.2023-0513
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The main sources of natural drugs include various biological species such as plants, animals, and microorganisms. The accurate identification of these species is the bedrock of natural drug development. We propose a novel method of species identification in this paper: analysis of whole-genome (AGE), a molecular diagnostic method used to identify species by finding species-specific sequences from the whole genome and precisely recognizing the specific target sequences. We elaborate that the principle for species identification based on AGE is that the genome sequences of diverse species must differ and divide the implementation strategy of the method into two levels of research and application. Based on our analysis of its characteristics, the method would have the potential advantages of reliable principle, high specificity, and wide applicability. Moreover, three crucial concerns related to building method systems including genome acquisition, bioinformatics analysis, and database construction, are further discussed. In summary, we offer theoretical underpinnings and methodological guidance for the development of bioinformatics software and commercial kits, indicating AGE has great application potential in objects, subjects, and industries.

analysis of whole-genome  /  species identification  /  whole genome  /  bioinformatics analysis  /  database construction
Yu-tong GAN, Tian-yi XIN, Wen-jie XU, Li-jun HAO, Gui-hong QI, Qian LOU, Jing-yuan SONG. Principles and strategies for species identification based on analysis of whole-genome[J]. Acta Pharmaceutica Sinica, 2023 , 58 (8) : 2364 -2374 . DOI: 10.16438/j.0513-4870.2023-0513
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Article Info
doi: 10.16438/j.0513-4870.2023-0513
  • Receive Date：2023-04-26
  • Online Date：2025-11-21
  • Published：2023-08-12
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History
  • Received：2023-04-26
  • Revised：2023-06-27
Funding
Affiliations
    1. Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
    2. Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
    3. Yunnan Branch, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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