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Outline
Natural components are crucial sources for drug discovery. Based on the central dogma of molecular biology, we proposed a novel paradigm for classifying natural products by categorizing natural components into "direct gene-encoded components" (including nucleic acids and peptides) and "indirect gene-encoded components" (encompassing primary metabolites and secondary metabolites). Utilizing multi-omics and artificial intelligence technologies, we systematically analyzed the nuclear and organellar genomes of 1 037 medicinal species sourced from eight authoritative global pharmacopeias, integrating multidimensional data resources to establish the gene-encoded natural diversity components repository (GNDC). This paper comprehensively describes: (1) The construction methodology of GNDC, including data integration strategies, standardized annotation pipelines, and rigorous quality control; (2) Core features and data scale: GNDC is currently the world's largest repository of medicinal natural products, housing over 234 million gene-encoded (directly or indirectly) natural components. It encompassed four specialized sub-databases: HerbalMDB for 2.32 million secondary metabolites, HerbalPDB for 229 million small peptides, HerbalRDB for 2.38 million small RNAs, and HerbalCDB for 0.26 million carbohydrates; (3) Exploring the application prospects of GNDC in the modernization of traditional medicine research. GNDC will provide an unprecedented expansive "chemical space" for drug discovery. It will powerfully drive a paradigm shift in drug development from "experience-oriented" to "big data-driven" approaches, offering a transformative framework for traditional medicine research.
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| 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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