ArticleBMC biology2020
Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants.
Article in BMC biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed, 155 citations in OpenAlex.
- Cell-Specific Expression and Cellular Compartmental Regulation in Camptothecin Biosynthesis.Plant biotechnology journal · 2026Article
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- Biosynthesis and heterologous production of the α-agarofuran scaffold of Celangulin V from Celastrus angulatus.Nature communications · 2026Article
- Identification and Characterization of Genes Associated With Wood Property Traits via Genome Sequencing in Fast-Growing Species of GenusEvolutionary applications · 2026Article
- DIMORPH: an integrated multi-omics resource for camptothecin-producing plants.Molecular horticulture · 2026Article
- Bioconversion of carotenoids into high-value crocins using a marine sponge carotenoid cleavage dioxygenase.The New phytologist · 2026Article
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Three Near telomere-to-telomere Genomes for Gardenia jasminoides.Scientific data · 2026Article
- Transcriptomics and Metabolomics Analysis Reveal the Mechanism of Petal Number Variation inMetabolites · 2026Article
- An evolutionarily diverged CCD4 enzyme negatively regulates mesocotyl elongation in rice.The New phytologist · 2026Article
- Physiological and transcriptomic insights into the molecular mechanisms of salt stress adaptation in Gardenia jasminoides.BMC plant biology · 2026Article
- Evolutionary adaptation of CCD4 enzymes inFrontiers in plant science · 2026Article
- Herbgenomics: Unraveling natural product biosynthesis in traditional Chinese medicine.Chinese herbal medicines · 2026Article
- Ancient gene clusters govern the initiation of monoterpenoid indole alkaloid biosynthesis and C3 stereochemistry inversion.Nature communications · 2025Article
- Montbretia flowers as a source of bioactive crocins: Biotechnology tools and delivery systems.Biotechnology reports (Amsterdam, Netherlands) · 2025Article
- Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.BMC genomics · 2025Article
- Application and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites.Plants (Basel, Switzerland) · 2025Review
- Water-soluble carotenoid: focused on natural carotenoid crocin.Food science and biotechnology · 2025Review
- A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation.GigaScience · 2025Article
- Biotechnological production of crocetin and crocins using a carotenoid cleavage dioxygenase (CCD4) fromFrontiers in plant science · 2025Article
23 more citing papers are in PubMed but not listed here.
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22 authors at 7 institutions in 6 countries.
Funding
Abstract
backgroundPlants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (Coffea, Camellia, Paullinia, and Ilex for caffeine; Crocus, Buddleja, and Gardenia for crocins) wherein they presumably evolved through convergent evolution. The closely related Coffea and Gardenia genera belong to the Rubiaceae family and synthesize, respectively, caffeine and crocins in their fruits.
resultsHere, we report a chromosomal-level genome assembly of Gardenia jasminoides, a crocin-producing species, obtained using Oxford Nanopore sequencing and Hi-C technology. Through genomic and functional assays, we completely deciphered for the first time in any plant the dedicated pathway of crocin biosynthesis. Through comparative analyses with Coffea canephora and other eudicot genomes, we show that Coffea caffeine synthases and the first dedicated gene in the Gardenia crocin pathway, GjCCD4a, evolved through recent tandem gene duplications in the two different genera, respectively. In contrast, genes encoding later steps of the Gardenia crocin pathway, ALDH and UGT, evolved through more ancient gene duplications and were presumably recruited into the crocin biosynthetic pathway only after the evolution of the GjCCD4a gene.
conclusionsThis study shows duplication-based divergent evolution within the coffee family (Rubiaceae) of two characteristic secondary metabolic pathways, caffeine and crocin biosynthesis, from a common ancestor that possessed neither complete pathway. These findings provide significant insights on the role of tandem duplications in the evolution of plant specialized metabolism.
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