Plant Reactome is a freely-accessible database of plant metabolic and regulatory pathways. Our goal is to provide plant researchers tools for visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. Our current version of Plant Reactome (Version 24, Gramene r69) was released in April 2025.

The development of Plant Reactome is supported the US National Science Foundation award (#1127112). The database is powered by the resources developed for the human Reactome project funded by the NIH (U41 HG003751) and the European Union 6th Framework Programme 'ENFIN'.

Selected Publications Citing Plant Reactome, Examples/Use Cases

• Virág E, Tóth BB, Kutasy B, Nagy Á, Pákozdi K, Pallos JP, Kardos G, Hegedűs G. Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in Arabidopsis Flowering Genes. Int J Mol Sci. 2025 Nov 18;26(22):11152. https://doi.org/10.3390/ijms262211152

• Yoosefzadeh-Najafabadi M. From text to traits: exploring the role of large language models in plant breeding. Front Plant Sci. 2025 May 14;16:1583344. | https://doi.org/10.3389/fpls.2025.1583344

• Murray SC, Verhoef A, Adak A, Sen D, Salzman R, Jaiswal P, Naithani S. Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing. Curr Opin Plant Biol. 2025 Feb;83:102684. https://doi.org/10.1016/j.pbi.2024.102684

• Sun, T. et al. TaCAMTA4 negatively regulates H2O2-dependent wheat leaf rust resistance by activating catalase 1 expression. Plant Physiol. 196, 2078-2088 (2024). https://doi.org:10.1093/plphys/kiae443

• Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes (Basel). 2024 Aug 14;15(8):1072. https://doi.org/10.3390/genes15081072

• Kruasuwan, W. et al. Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces. Rice (N Y) 16, 6 (2023). https://doi.org:10.1186/s12284-023-00622-7

• Dussarrat, T. et al. Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. New Phytol 234, 1614-1628 (2022).https://doi.org:10.1111/nph.18095

• Wu L, Fredua-Agyeman R, Strelkov SE, Chang KF, Hwang SF. Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis. Int J Mol Sci. 2022 Aug 28;23(17):9744. https://doi.org/10.3390/ijms23179744

• Subudhi, P. K., Garcia, R. S., Coronejo, S. & Tapia, R. Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture. International journal of molecular sciences 21 (2020). https://doi.org:10.3390/ijms21165759