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PMhub 1.0: a comprehensive plant metabolome database.
Zhitao Tian1,2, Xin Hu1,2, Yingying Xu1,2
1National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
Nucleic Acids Research
|October 11, 2023
Summary
The Plant Metabolome Hub (PMhub) is a comprehensive database for plant metabolite information, including spectra, genetics, and pathways. It integrates diverse data, enabling advanced plant metabolomics research.
Area of Science:
- Plant Science
- Metabolomics
- Bioinformatics
Background:
- Plant metabolomics research requires integrated access to metabolite data, spectra, and genetic information.
- Existing databases often lack comprehensive data integration or experimental validation.
Purpose of the Study:
- To introduce the Plant Metabolome Hub (PMhub), a unified resource for plant metabolite data.
- To provide tools for analyzing metabolite networks, genetic underpinnings, and experimental data.
Main Methods:
- Data aggregation from literature and experimental sources.
- Generation of in-silico high-resolution tandem mass-spectrometry (HRMS/MS) spectra.
- Network reconstruction based on structural similarity and metabolic pathways.
- Integration of genomic and transcriptomic data.
- In vitro enzymatic activity experiments for pathway validation.
Main Results:
- PMhub houses data for 188,837 plant metabolites with 1,467,041 HRMS/MS spectra.
- Includes 144,366 detected experimental features across 10 plant species, with 16,423 annotated.
- Successfully validated a synthetic pathway for N-p-coumaroyltyramine.
Conclusions:
- PMhub offers a robust platform for plant metabolomics research by integrating diverse data types.
- The database facilitates comprehensive genetic analysis of plant metabolites.
- PMhub serves as an indispensable tool for the plant science community.
