![]() Unlike coffee, gardenia does not accumulate caffeine. jasminoides, whose major bioactive constituents are genipin and crocins, were used as an imperial dye for royal costumes during the Qin and Han dynasties in China and are recorded in the Chinese Pharmacopoeia. The Chinese species Gardenia jasminoides (gardenia) has been cultivated for at least 1000 years and was introduced to Europe and America in the mid-eighteenth century. In this large family of angiosperms, only the Coffea canephora (robusta coffee) genome has been sequenced to date. The Gardenia genus, which is among the most commonly grown horticultural plants worldwide and is valued for the strong, sweet fragrance of its flowers, belongs to the family Rubiaceae. Given the ongoing nature of CNV production during evolution, genome sequencing of closely related plants harboring distinct secondary metabolite profiles holds great promise for understanding the stepwise evolution of important tandem duplicate clusters. Tandem gene duplicate clusters originally arise as copy number variants (CNVs) in populations that later become fixed within species by evolving split or novel functions. A few important metabolic clusters involve only tandem duplicates within single gene families, such as the N-methyltransferase ( NMT) genes that control caffeine biosynthesis in the coffee plant, and the cytochrome p450 genes encoding the 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) metabolic cluster of maize, which produces an important defense compound. In many cases, the genomic context for the evolution of specialized plant compounds involves tightly linked clusters of genes, usually containing nonhomologous gene families, that together control novel biosynthetic pathways. These findings provide significant insights on the role of tandem duplications in the evolution of plant specialized metabolism.įlowering plants have evolved a diverse array of secondary metabolites to repel pathogens and predators, attract pollinators, and drive ecosystem functions. This 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. 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. 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. Through genomic and functional assays, we completely deciphered for the first time in any plant the dedicated pathway of crocin biosynthesis. Here, we report a chromosomal-level genome assembly of Gardenia jasminoides, a crocin-producing species, obtained using Oxford Nanopore sequencing and Hi-C technology. The closely related Coffea and Gardenia genera belong to the Rubiaceae family and synthesize, respectively, caffeine and crocins in their fruits. 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. ![]() Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. ![]()
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