RefMetaPlant: a reference metabolome database for plants across five major phyla

Abstract Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stre...

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Bibliographic Details
Published in:Nucleic acids research 2024-01, Vol.52 (D1), p.D1614-D1628
Main Authors: Shi, Han, Wu, Xueting, Zhu, Yan, Jiang, Tao, Wang, Zhengwei, Li, Xuetong, Liu, Jianju, Zhang, Yingxue, Chen, Feng, Gao, Jinshan, Xu, Xiaoyan, Zhang, Guoqing, Xiao, Ning, Feng, Xianzhong, Zhang, Peng, Wu, Yongrui, Li, Aihong, Chen, Ping, Li, Xuan
Format: Article
Language:English
Subjects:
Chromatography, Liquid
Databases, Factual
Metabolome - genetics
Metabolomics - methods
Plants - metabolism
Tandem Mass Spectrometry
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Summary:Abstract Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC–MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A ‘Reference Metabolome Database for Plants’ (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like ‘LC–MS/MS Query’, ‘RefMetaBlast’ and ‘CompoundLibBlast’ for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/. Graphical Abstract Graphical Abstract
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad980