ArticlePlant physiology2017
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.
Article in Plant physiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 178 papers.
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Who cites it
178 citing papers in PubMed, 379 citations in OpenAlex.
- Single-Cell Insights into Medicinal Plant Development and Metabolism.Plants (Basel, Switzerland) · 2026Review
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- Metabolite correlation-based network analysis combined with machine learning techniques highlights LOX biosynthesis in Vanilla planifolia and Vanilla pompona source leaves.Scientific reports · 2026Article
- The Phenylpropanoid Pathway Is a Central Roundabout in Peach Fruit Pre- and Postharvest Physiology.Metabolites · 2026Article
- Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy.The Plant cell · 2026Article
- Regulatory network rewiring drives strain-specific lipid accumulation response in Chlorella sorokiniana under nutrient starvation.The Plant journal : for cell and molecular biology · 2026Article
- Identification of Stress-Induced Biosynthetic Gene Clusters in Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- C11orf54 catalyzes L-xylulose formation in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways.PLoS biology · 2025Article
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- Genome-wide terpene gene clusters analysis in Euphorbiaceae.Horticulture research · 2025Article
- Independent evolution of betulin biosynthesis in Inonotus obliquus.Scientific reports · 2025Article
- The ins and outs of plant specialized metabolite gene organization.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A long road ahead to reliable and complete medicinal plant genomes.Nature communications · 2025Review
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- Integrative physiological, biochemical, and metabolomic analyses reveal complex drought and zinc stress tolerance in a novelFrontiers in plant science · 2025Article
- Genome mining of metabolic gene clusters in the Rubiaceae family.Computational and structural biotechnology journal · 2024Article
118 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
12 authors at 2 institutions in 3 countries.
Funding
Abstract
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.