HMOD: An Omics Database for Herbal Medicine Plants

Wang, Xiao; Zhang, Jiajin; He, Simei; Gao, Yuanni; Ma, Xiaoqin; Gao, Yun; Zhang, Guanghui; Kui, Ling; Wang, Wen; Wang, Ying; Yang, Shengchao; Dong, Yang

doi:10.1016/j.molp.2018.03.002

Cited by 26 publications

(16 citation statements)

References 9 publications

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“…The GPGD is the first online system aimed at regulated herbs recorded in pharmacopoeias on the global market. Therefore, the utilization of "omics" data for the authentication, cultivation, and breeding of herbs sets the GPGD apart from common scienceor interest-oriented medicinal species databases (Fang et al, 2021;Ru et al, 2014;Wang et al, 2018;Xue et al, 2013). The GPGD can be extensively used for herb research, thus contributing to global human health.…”

Section: Discussionmentioning

confidence: 99%

Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

Liao

Xiao

et al. 2021

Sci. China Life Sci.

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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. Supporting Information The supporting information is available online at 10.1007/s11427-021-1968-7. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.

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Section: Discussionmentioning

confidence: 99%

Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

Liao

Xiao

et al. 2021

Sci. China Life Sci.

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“…We found that the NAPRALERT ® database ( ), IMPPAT ® ( ) or TCMID ® ( ) were particularly interesting, since these include data from the literature on natural products, pharmacological/biochemical bioactivities and ethnomedical information. Databases displaying a more molecular tendency are, for example, the Herbal Medicine Omics Database (HMOD) and the Plant Metabolic Network (PMN), that integrate metabolic and biochemical data with publicly available genomic, transcriptomics and enzymatic databases [ 20 , 21 ]. These data may serve as the basis for in silico processing and to computationally reconstruct a single specific pathway, and thus assess the broader roles of the structural genes involved in the pathway of interest and to facilitate the discovery of new enzymes.…”

Section: Molecules In Crop and Medicinal Plants: The Evolution Of Their Usementioning

confidence: 99%

Specialized Metabolites and Valuable Molecules in Crop and Medicinal Plants: The Evolution of Their Use and Strategies for Their Production

D’Amelia

Docimo

Crocoll

et al. 2021

Genes

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Plants naturally produce a terrific diversity of molecules, which we exploit for promoting our overall well-being. Plants are also green factories. Indeed, they may be exploited to biosynthesize bioactive molecules, proteins, carbohydrates and biopolymers for sustainable and large-scale production. These molecules are easily converted into commodities such as pharmaceuticals, antioxidants, food, feed and biofuels for multiple industrial processes. Novel plant biotechnological, genetics and metabolic insights ensure and increase the applicability of plant-derived compounds in several industrial sectors. In particular, synergy between disciplines, including apparently distant ones such as plant physiology, pharmacology, ‘omics sciences, bioinformatics and nanotechnology paves the path to novel applications of the so-called molecular farming. We present an overview of the novel studies recently published regarding these issues in the hope to have brought out all the interesting aspects of these published studies.

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“…The Herbal Medicine Omics Database 103 includes genomic, transcriptomic, pathway, and metabolomic data for medicinal plants, although the medicinal properties of some plants are recognized only in some parts of the world. In this database, hundreds of medicinal plants are included.…”

Section: Data Storage and Visualizationmentioning

confidence: 99%

Genome sequences of horticultural plants: past, present, and future

et al. 2019

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Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.

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HMOD: An Omics Database for Herbal Medicine Plants

Cited by 26 publications

References 9 publications

Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

Specialized Metabolites and Valuable Molecules in Crop and Medicinal Plants: The Evolution of Their Use and Strategies for Their Production

Genome sequences of horticultural plants: past, present, and future

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