Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants

Background Plants 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, andIlexfor caffeine;Crocus,Buddleja, andGardeniafor crocins) wherein they presumably evolved through convergent evolution. The closely relatedCoffeaandGardeniagenera belong to the Rubiaceae family and synthesize, respectively, caffeine and crocins in their fruits. Results Here, we report a chromosomal-level genome assembly ofGardenia 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 withCoffea canephoraand other eudicot genomes, we show thatCoffeacaffeine synthases and the first dedicated gene in theGardeniacrocin pathway,GjCCD4a, evolved through recent tandem gene duplications in the two different genera, respectively. In contrast, genes encoding later steps of theGardeniacrocin pathway, ALDH and UGT, evolved through more ancient gene duplications and were presumably recruited into the crocin biosynthetic pathway only after the evolution of theGjCCD4agene. Conclusions 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. These findings provide significant insights on the role of tandem duplications in the evolution of plant specialized metabolism.