Plant metabolites play an important role in plant growth, development, and adaptation to the environment. Comparing metabolite differences between different species provides an effective strategy for exploring important genes and excellent germplasm resources, exploring metabolic pathways, and analyzing the formation of complex traits. However, existing plant metabolite-related databases mostly focus on integrating metabolite information and related metabolic pathways within small-scale species, and fail to fully tap the research potential brought by metabolite differences across species. In addition, the coding system of metabolites in various databases lacks consistency, resulting in high data heterogeneity and weak correlation, which makes it difficult to directly use for comparative metabolome analysis. Based on this, in order to further improve the understanding of metabolite diversity among different plants, a standardized comprehensive platform is urgently needed to achieve comparative metabolome analysis across species.
On July 10, 2024, the bioinformatics team of Huazhong Agricultural University published a research result entitled "PCMD: A multilevel comparison database of intra- and cross-species metabolic profiling in 530 plant species" in Plant Communications. Based on the metabolic networks, metabolites, reactions and rich species classification information of 530 plants, this study built the plant comparative metabolome database (PCMD; http://yanglab.hzau.edu.cn/PCMD), which provides valuable resources and analysis platforms for promoting plant comparative metabolomics research.
This study used the genome-scale metabolic model (GEM) to construct metabolic networks of 530 plants and predicted plant metabolites and reaction formulas. Further information on basic plant information and classification, metabolite information, experimentally determined metabolites, and related literature was collected. PCMD contains a total of 213,264 metabolites, 30,669 experimentally determined metabolites, 8,384 enzymes, 8,678 reaction formulas, and 33,397 literature. Users can query, obtain, and analyze the above data by accessing six modules in PCMD, including Species, Metabolites, Reaction, Literature, Download, and Help.
Figure 1. Overview of PCMD. (Hu, et al., 2024)
PCMD provides a multi-level analysis platform for cross-species comparative metabolome research, involving multiple levels such as species, metabolites, metabolic pathways, and biological taxonomy.
Diversify species searches to explore plant metabolic characteristics. By using the "Search Species" page of the "Species" module, users can search for the scientific name, common name, and abbreviation of plants to obtain their metabolite characteristic information, and can use the "Species List" page to view the distribution of 530 plants ranked according to the number of their metabolites, enzymes, and reactions, thereby deepening the understanding of the metabolic characteristics of each plant.
Diversify the classified species information and compare the metabolite differences between species. Using the "Species-comparison" tool, users can compare the specificity and commonality of metabolites between two different groups of plants based on the selected classification information (including species classification, reproductive characteristics, seed and leaf characteristics, and domestication information) or upload a list of plant names.
Personalized upload of metabolites to reveal the enrichment distribution of metabolites. Using the "Metabolite-enrichment" tool, users can upload a specified list of metabolites to further explore in which species these metabolites are enriched.
In addition, PCMD provides a highly standardized platform for metabolite comparison. By integrating the resources of 17 existing metabolite databases, including Biocyc, PubChem, CHEBI, KEGG, CAS, ChEMBL, MetanetX, NIKKAJI, KNApSAcK, 3DMET, ChemSpider, SEED, PDB-CCD, HMDB, BiGG, Metabolights, and PMhub, PCMD achieves unified recoding of metabolites and establishes a standardized system. On this basis, the "Metabolite ID-conversion" tool was developed, allowing users to quickly and efficiently convert the IDs of metabolites in the above databases, thereby achieving effective integration and utilization of metabolic data from different sources.
Based on the constructed PCMD database, the researchers used the "Species-comparison" tool to conduct a case study on the metabolite differences between Brassica and Solanum genera. The results showed that α-chaconine and α-solanine are specifically present in Solanum genus. Further enrichment analysis found that Brassica genus may lack the pathway to convert 16,22,26-trihydroxycholesterol into solanidine, which in turn leads to impaired synthesis of α-chaconine and α-solanine. The analysis of metabolite differences between Brassica and Solanum genera not only provides a valuable reference for understanding the biochemical differences between these two types of plants, but also demonstrates the ability of PCMD in revealing the diversity of metabolites among plants.
In summary, PCMD is currently the most species-rich plant comparative metabolome database, providing rich metabolite resources and analysis tools, which helps researchers to have a more comprehensive understanding of the metabolite differences between species and provides a new perspective for exploring the diversity of metabolites among species.
