Abstract
Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However, the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database (GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias (Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.
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Alaux, M., Rogers, J., Letellier, T., Flores, R., Alfama, F., Pommier, C., Mohellibi, N., Durand, S., Kimmel, E., Michotey, C., et al. (2018). Linking the international Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol 19, 111.
Atanasov, A.G., Waltenberger, B., Pferschy-Wenzig, E.M., Linder, T., Wawrosch, C., Uhrin, P., Temml, V., Wang, L., Schwaiger, S., Heiss, E. H., et al. (2015). Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotech Adv 33, 1582–1614.
Bantawa, P., Ghosh, S.K., Maitra, S., Ghosh, P.D., and Mondal, T.K. (2009). Status and conservation threats of Picrorhiza scrophulariiflora Pennell. (Scrophulariaceae): An endangered high valued medicinal plant of Indo-China Himalayan region. Bioremed Biodivers Bioavailab 3, 15–22.
Buels, R., Yao, E., Diesh, C.M., Hayes, R.D., Munoz-Torres, M., Helt, G., Goodstein, D.M., Elsik, C.G., Lewis, S.E., Stein, L., et al. (2016). JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17, 66.
Callaway, E., and Cyranoski, D. (2015). Anti-parasite drugs sweep Nobel prize in medicine 2015. Nature 526, 174–175.
Campbell, M.S., Law, M.Y., Holt, C., Stein, J.C., Moghe, G.D., Hufnagel, D.E., Lei, J., Achawanantakun, R., Jiao, D., Lawrence, C.J., et al. (2014). MAKER-P: A tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol 164, 513–524.
Chan, T.Y.K. (2002). Incidence of herb-induced aconitine poisoning in Hong Kong. Drug Saf 25, 823–828.
Chen, S., Pang, X., Song, J., Shi, L., Yao, H., Han, J., and Leon, C. (2014). A renaissance in herbal medicine identification: from morphology to DNA. Biotech Adv 32, 1237–1244.
Chen, S., Su, G., Zou, J., Huang, L., Guo, B., and Xiao, P. (2005). The sustainable development framework of national Chinese medicine resources (in Chinese). China J Chin Mater Med 30, 1141–1146.
Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., Pang, X., et al. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE 5, e8613.
Chen, X., Zhou, J., Cui, Y., Wang, Y., Duan, B., and Yao, H. (2018). Identification of Ligularia Herbs using the complete chloroplast genome as a super-barcode. Front Pharmacol 9, 695.
Chik, W.I., Zhu, L., Fan, L.L., Yi, T., Zhu, G.Y., Gou, X.J., Tang, Y.N., Xu, J., Yeung, W.P., Zhao, Z.Z., et al. (2015). Saussurea involucrata: A review of the botany, phytochemistry and ethnopharmacology of a rare traditional herbal medicine. J Ethnopharmacol 172, 44–60.
Coordinating Research Group for the Structure of Artemisinin. (1977). Artemisinin: A new type of sesquiterpene lactone (in Chinese). Chin Sci Bull 22, 142.
Cordell, G.A. (2015). Ecopharmacognosy and the responsibilities of natural product research to sustainability. Phytochem Lett 11, 332–346.
Dong, L., Chen, Z., Wang, Y., Wei, F., Zhang, L., Xu, J., Wei, G., Wang, R., Yang, J., and Liu, W. (2017). DNA marker-assisted selection of medicinal plants (I). Breeding research of disease-resistant cultivars of Panax notoginseng (in Chinese). China J Chin Mater Med 42, 56–62.
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S.R., Luciani, A., Potter, S.C., Qureshi, M., Richardson, L.J., Salazar, G.A., Smart, A., et al. (2018). The Pfam protein families database in 2019. Nucleic Acids Res 47, D427–D432.
Fang, S.S., Dong, L., Liu, L., Guo, J.C., Zhao, L.H., Zhang, J.Y., Bu, D.C., Liu, X.K., Huo, P.P., Cao, W.C., et al. (2021). HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. Nucleic Acids Res 49, D1197–D1206.
Geuna, F. (2017). Molecular-assisted breeding. In: Pilu, R., and Gavazzi, G., eds. More Food: Road to Survial. Sharjah: Bentham Science Publishers. 373–398.
Gilbert, N. (2011). Regulations: Herbal medicine rule book. Nature 480, S98–S99.
Guan, Z., Li, Z., and Li, E. (2002). A rare and endangered medicinal plant: Dendrobium nobile (in Chinese). Chin Wild Plant Resour 21, 36–37.
Guo, L., Winzer, T., Yang, X., Li, Y., Ning, Z., He, Z., Teodor, R., Lu, Y., Bowser, T.A., Graham, I.A., et al. (2018). The opium poppy genome and morphinan production. Science 362, 343–347.
Guo, M., Ren, L., Xu, Y., Liao, B., Song, J., Li, Y., Mantri, N., Guo, B., Chen, S., and Pang, X. (2019). Development of plastid genomic resources for discrimination and classification of Epimedium wushanense (Berberidaceae). Int J Mol Sci 20, 4003.
Han, J., Pang, X., Liao, B., Yao, H., Song, J., and Chen, S. (2016). An authenticity survey of herbal medicines from markets in China using DNA barcoding. Sci Rep 6, 18723.
Hebert, P.D.N., Cywinska, A., Ball, S.L., and deWaard, J.R. (2003). Biological identifications through DNA barcodes. Proc R Soc Lond B 270, 313–321.
Hu, H., Shen, X., Liao, B., Luo, L., Xu, J., and Chen, S. (2019). Herbgenomics: A stepping stone for research into herbal medicine. Sci China Life Sci 62, 913–920.
Huang, D.I., and Cronk, Q.C.B. (2015). Plann: A command-line application for annotating plastome sequences. Appl Plant Sci 3, 1500026.
Jackman, S.D., Vandervalk, B.P., Mohamadi, H., Chu, J., Yeo, S., Hammond, S.A., Jahesh, G., Khan, H., Coombe, L., Warren, R.L., et al. (2017). ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 27, 768–777.
Jin, J., Tian, F., Yang, D.C., Meng, Y.Q., Kong, L., Luo, J., and Gao, G. (2016). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45, D1040–D1045.
Jones, P., Binns, D., Chang, H.Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., et al. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240.
Kim, N.H., Jayakodi, M., Lee, S.C., Choi, B.S., Jang, W., Lee, J., Kim, H. H., Waminal, N.E., Lakshmanan, M., van Nguyen, B., et al. (2018). Genome and evolution of the shade-requiring medicinal herb Panax ginseng. Plant Biotechnol J 16, 1904–1917.
Li, J., Wang, S., Yu, J., Wang, L., and Zhou, S. (2013). A modified CTAB protocol for plant DNA extraction. Chin Bull Bot 48, 72–78.
Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y., and Chen, S. (2015). Plant DNA barcoding: from gene to genome. Biol Rev 90, 157–166.
Liang, H.H., Cheng, Z., Yang, X.L., Li, S., Ding, Z.Q., Zhou, T.S., Zhang, W.J., and Chen, J.K. (2008). Genetic diversity and structure of Cordyceps sinensis populations from extensive geographical regions in China as revealed by inter-simple sequence repeat markers. J Microbiol 46, 549–556.
Lowe, L., Matteucci, M.J., and Schneir, A.B. (2005). Herbal aconite tea and refractory ventricular tachycardia. N Engl J Med 353, 1532.
Lu, J., and Lan, X. (2013). An investigation on rare and endangered Tibetan medicinal plants in Lhasa region (in Chinese). China J Chin Mater Med 38, 127–132.
Luo, L., Jiang, J., Wang, C., Fitzgerald, M., Hu, W., Zhou, Y., Zhang, H., and Chen, S. (2020). Analysis on herbal medicines utilized for treatment of COVID-19. Acta Pharm Sin B 10, 1192–1204.
Lv, Q., Qiu, J., Liu, J., Li, Z., Zhang, W., Wang, Q., Fang, J., Pan, J., Chen, Z., Cheng, W., et al. (2020). The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis. Plant J 103, 1910–1923.
Meng, G., Li, Y., Yang, C., and Liu, S. (2019). MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res 47, e63.
Mount, D.W. (2007). Using the basic local alignment search tool (BLAST). Cold Spring Harb Protoc 2007(7), pdb.top17.
Muniraj, N., Siddharth, S., and Sharma, D. (2019). Bioactive compounds: Multi-targeting silver bullets for preventing and treating breast cancer. Cancers 11, 1563.
Newman, D.J., and Cragg, G.M. (2020). Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J Nat Prod 83, 770–803.
Osuna-Cruz, C.M., Paytuvi-Gallart, A., Di Donato, A., Sundesha, V., Andolfo, G., Aiese Cigliano, R., Sanseverino, W., and Ercolano, M.R. (2017). PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. Nucleic Acids Res 46, D1197–D1201.
Pertea, M., Kim, D., Pertea, G.M., Leek, J.T., and Salzberg, S.L. (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650–1667.
Pešić, M. (2015). Development of natural product drugs in a sustainable manner. In: Brief for United Nations Global Sustainable Development Report 2015.
Poon, W.T., Lai, C.K., Ching, C.K., Tse, K.Y., So, Y.C., Chan, Y.C., Hau, L. M., Mak, T.W.L., and Chan, A.Y.W. (2006). Aconite poisoning in camouflage. Hong Kong Med J 12, 456–459.
Portwood, J.L., Woodhouse, M.R., Cannon, E.K., Gardiner, J.M., Harper, L.C., Schaeffer, M.L., Walsh, J.R., Sen, T.Z., Cho, K.T., Schott, D.A., et al. (2019). MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Res 47, D1146–D1154.
Ru, J., Li, P., Wang, J., Zhou, W., Li, B., Huang, C., Li, P., Guo, Z., Tao, W., Yang, Y., et al. (2014). TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J Cheminform 6, 1–6.
Shen, Q., Zhang, D., Sun, W., Zhang, Y., Shang, Z., and Chen, S. (2017a). Medicinal plant DNA marker assisted breeding (II) the assistant identification of SNPs assisted identification and breeding research of high yield Perilla frutescens new variety (in Chinese). China J Chin Mater Med 42, 1668–1672.
Shen, X., Wu, M., Liao, B., Liu, Z., Bai, R., Xiao, S., Li, X., Zhang, B., Xu, J., and Chen, S. (2017b). Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Molecules 22, 1330.
Smanski, M.J., Zhou, H., Claesen, J., Shen, B., Fischbach, M.A., and Voigt, C.A. (2016). Synthetic biology to access and expand nature’s chemical diversity. Nat Rev Microbiol 14, 135–149.
Tareke Woldegiorgis, S., Wang, S., He, Y., Xu, Z., Chen, L., Tao, H., Zhang, Y., Zou, Y., Harrison, A., Zhang, L., et al. (2019). Rice stress-resistant SNP database. Rice 12, 97.
Vadakkemukadiyil Chellappan, B., Pr, S., Vijayan, S., Rajan, V.S., Sasi, A., and Nair, A.S. (2019). High quality draft genome of Arogyapacha (Trichopus zeylanicus), an important medicinal plant endemic to Western Ghats of India. G3 9, 2395–2404.
Wang, X., Zhang, J., He, S., Gao, Y., Ma, X., Gao, Y., Zhang, G., Kui, L., Wang, W., Wang, Y., et al. (2018). HMOD: an omics database for herbal medicine plants. Mol Plant 11, 757–759.
Weaver, B.A. (2014). How Taxol/paclitaxel kills cancer cells. Mol Bio Cell 25, 2677–2681.
World Health Organization. (2013). The international pharmacopoeia. WHO Drug Inf 27, 119–128.
World Health Organization. (2019). Index of Pharmacopoeias. Geneva: World Health Organization.
Xiao, P., Zhao, R., Long, X., and Guo, B. (2009). Macroscopic analysis on production and marketing of medicinal material resources for sustainable development (in Chinese). China J Chin Mater Med 34, 2135–2139.
Xu, J., Chu, Y., Liao, B., Xiao, S., Yin, Q., Bai, R., Su, H., Dong, L., Li, X., Qian, J., et al. (2017). Panax ginseng genome examination for ginsenoside biosynthesis. Gigascience 6, gix093.
Xue, R., Fang, Z., Zhang, M., Yi, Z., Wen, C., and Shi, T. (2013). TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res 41, D1089–D1095.
Acknowledgements
This work was supported by the National Key Research and Development Program of China (2019YFC1711100), the National Natural Science Foundation of China and Karst Science Research Center of Guizhou Province (U1812403-1), the Special Foundation for National Science and Technology Basic Research Program of China (2018FY100701), the Fundamental Research Funds for the Central Public Welfare Research Institutes (ZXKT17027, ZXKT18014), the Open Research Fund of Chengdu University of Traditional Chinese Medicine Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China (2020GZ2011016), the Funds for Fostering Outstanding Scholars in Science and Technology (Innovation) (ZZ13-YQ-047), and Innovation Fund of China Academy of Chinese Medical Sciences. The authors thank Professor Salwa El-Hallouty and Professor Rehab Ahmed (Department of Pharmacognosy, National Research Center, Egypt) for providing medicinal species information from the Egyptian Pharmacopoeia. We also thank Professor Baozhong Duan (College of Pharmaceutical Science, Dali University), Professor Dianyun Hou (Agricultural College, Henan University of Science and Technology), Dr. Qinghua Wu (Chengdu University of Traditional Chinese Medicine), Professor Xiaojun Zhang (Heilongjiang Mudanjiang Normal University), Dr. Weisi Ma, and Fuhe Chen for providing medicinal species samples.
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Liao, B., Hu, H., Xiao, S. et al. Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. Sci. China Life Sci. 65, 809–817 (2022). https://doi.org/10.1007/s11427-021-1968-7
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DOI: https://doi.org/10.1007/s11427-021-1968-7