ArticleThe Plant cell2017
A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants.
Article in The Plant cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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123 citing papers in PubMed.
- Archipelago architecture and evolution of paclitaxel biosynthesis revealed by the Pseudotaxus chienii haplotype-resolved genome.Nature communications · 2026Article
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- Nitrogen Status Rewires Transcriptional Regulation of Dhurrin, a Dual-Purpose Defense Metabolite inPlant direct · 2026Article
- Host-Botrytis co-transcriptomics reveals finely tuned interactions with closely related legumes.G3 (Bethesda, Md.) · 2026Article
- Coexpression network analysis reveals the genetic basis of divergent lipid and sugar accumulation in peanut (Food chemistry. Molecular sciences · 2026Article
- Functional insights into dispensable genes using genome-wide loss-of-function burden tests in Arabidopsis.The Plant cell · 2026Article
- Chemically guided single-cell transcriptomics reveals sulfotransferase-mediated scaffold remodeling in securinine biosynthesis.Nature communications · 2026Article
- An integrated transcriptomic and metabolomic atlas reveals the temporal regulation of benzylisoquinoline alkaloid biosynthesis and transport in developing opium poppy capsules.Frontiers in plant science · 2026Article
- Mechanistic Perspectives From Genomics and Pangenomics of Medicinal and Aromatic Plants: Linking Genome Architecture to Phytochemical Diversity.International journal of genomics · 2026Review
- A cell-type-specific regulon controlling monoterpene indole alkaloid biosynthesis with feedback and feedforward activation loops.The New phytologist · 2026Article
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.Frontiers in plant science · 2026Review
- Genome-wide terpene gene clusters analysis in Euphorbiaceae.Horticulture research · 2025Article
- MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways.PLoS biology · 2025Article
- From data to discovery: leveraging big data in plant natural products biosynthesis research.The Plant journal : for cell and molecular biology · 2025Review
- Entry Steps in the Biosynthetic Pathway to Diterpenoid Alkaloids inbioRxiv : the preprint server for biology · 2025Article
- Multi-omics analysis reveals tissue-specific biosynthesis and accumulation of diterpene alkaloids in Aconitum japonicum.Journal of natural medicines · 2025Article
- The aerial epidermis is a major site of quinolizidine alkaloid biosynthesis in narrow-leafed lupin.The New phytologist · 2025Article
- Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae.American journal of botany · 2025Article
- Evolution of plant metabolism: the state-of-the-art.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
63 more citing papers are in PubMed but not listed here.
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global coexpression data sets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of coexpressed gene modules per data set. In support of our hypothesis, 15.3 to 52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e., those lacking an associated metabolite) were no more coexpressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene coexpression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products.
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