This App takes a Genome object as the input and uses OrthoFinder to cluster transcripts with Arabidopsis enzymes curated in PlantSEED. It also annotates the protein-coding genes with metabolic functions and provides the annotated Genome object as an output. Each of the Arabidopsis enzymes are used as the initial member of each cluster, and every transcript in the selected genome is placed within the same cluster if it meets two main criteria: (i) the sequence identity of the transcript-enzyme pair is higher than the other transcript-enzyme pairs and (ii) the sequence identity of the transcript-enzyme pair meets the selected threshold. More details on this selection process can be found in the publications. Once placed in a cluster, the metabolic function of the enzyme is propagated to the transcripts in the same cluster. The annotations are linked to biochemical reactions, and researchers may use the Reconstruct Plant Metabolism App to follow up and build a working model of plant primary metabolism.

• Arabidopsis thaliana TAIR10
• Amborella trichopoda v1.0
• Brachypodium distachyon v3.1
• Chlamydomonas reinhardtii v5.6
• Citrus sinensis v1.1
• Glycine max Wm82.a4.v1
• Malus domestica v1.0
• Ostreococcus lucimarinus v2.0
• Oryza sativa v7.0
• Populus trichocarpa v4.1
• Sorghum bicolor v3.1.1
• Solanum lycopersicum ITAG3.2
• Selaginella moellendorffii v1.0
• Spirodela polyrhiza v2
• Zea mays RefGen V4

• PlantSEED
• The plant metabolic subsystems are curated as part of the PlantSEED project. The curation can be explored here

• OrthoFinder version 2.5.2
• Diamond version 2.0.9