Hu, Y.; Ruan, Y.; Zhao, X.-L.; Jiang, F.; Zhu, Q.; Zhang, Q.-Y.; Qing-Yong, Y.

Comparative metabolomics plays a crucial role in understanding gene function, exploring metabolite evolution, and improving crop genetic breeding. However, a systematic platform for comparing intra- and cross-species metabolites is currently lacking. In this study, we present the plant comparative metabolome database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a comprehensive multi-level comparison database encompassing intra- and cross-species metabolic profiling in 530 plants. Remarkably, PCMD offers a multi-level platform for comparative metabolite analysis, allowing for the examination of metabolite characteristics across species at various levels including species, metabolites, pathways, and biological taxonomy. In addition, PCMD standardizes metabolite numbering, establishing a uniform system based on existing metabolite-related databases. The database also provides a range of user-friendly online tools, such as Species-comparison, Metabolites-enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. PCMD stands out as the most comprehensive and species-rich comparative plant metabolomics database currently available, as demonstrated by two case studies that highlight its ability to supplement phylogenetic similarity mining among species through phylogenetic trees and offer new insights into the diversity and species-specificity of metabolites.