FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Authors: XU, CHUNHUI - University Of Missouri; SHAW, TREY - University Of Missouri; CHOPPARARU, SAI AKHIL - University Of Missouri; LU, YIWEI - University Of Missouri; FAROOQ, SHAIK NAVEED - University Of Missouri; QIN, YONGFANG - University Of Missouri; HUDSON, MATT - University Of Missouri; WEEKLEY, BROCK - University Of Missouri; FISHER, MICHAEL - University Of Missouri; HE, FEI - University Of Missouri; NASCIMENTO, JOSE ROBERTO DA - University Of Missouri; WERGELES, NICHOLAS - University Of Missouri; JOSHI, TRUPTI - University Of Missouri; BATES, PHILIP - Washington State University; KOO, ABARAHAM - University Of Missouri; Allen, Douglas - Doug; CAHOON, EDGAR - University Of Nebraska; THELEN, JAY - University Of Missouri; XU, DONG - University Of Missouri

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2024
Publication Date: 8/5/2024
Citation: Xu, C., Shaw, T., Choppararu, S., Lu, Y., Farooq, S., Qin, Y., Hudson, M., Weekley, B., Fisher, M., He, F., Nascimento, J.S., Wergeles, N., Joshi, T., Bates, P.D., Koo, A.J., Allen, D.K., Cahoon, E.B., Thelen, J.J., Xu, D. 2024. FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants. Database: The Journal of Biological Databases and Curation. 2024. https://doi.org/10.1093/database/baae074.
DOI: https://doi.org/10.1093/database/baae074

Interpretive Summary: Vegetable oils are an energy dense renewable feed stock for chemical, fuels and are an essential component of the human diet. It is estimated that by 2050, the current production of vegetable oil will need to double to meet societal needs. Our understanding of lipid biosynthetic pathways in plants remains limited and would benefit from web resources that are capable of organizing existing data related lipid metabolism. Although some online platforms have been developed to curate plant acyl-lipid metabolism, frequently these resources are limited in scope or outdated. To assist researchers in studying plant fatty acid metabolism efficiently, we have developed a one-stop-shop web resource solution, FatPlants. Our online web resource provides chemical molecular structures and physical properties and links information related to metabolic pathways, enzymes, and genes to enable scientists to understand the biology of lipids so that crops can be augmented to produce higher lipid levels for the benefit of humankind.

Technical Abstract: FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/