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, 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. Results: Here, 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.

The in-depth understanding of the minority phases' roles in functional materials, e.g., batteries, is critical for optimizing the system performance and the operational efficiency. Although the visualization of battery electrode under operating conditions has been demonstrated, the development of advanced data-mining approaches is still needed in order to identify minority phases and to understand their functionalities. The present study uses nanoscale X-ray spectromicroscopy to study a functional LiCoO/Li battery pouch cell. The data-mining approaches developed herein were used to search through over 10 million X-ray absorption spectra that cover more than 100 active cathode particles. Two particles with unanticipated chemical fingerprints were identified and further analyzed, providing direct evidence and valuable insight into the undesired side reactions involving the cation dissolution and precipitation as well as the local overlithiation-caused subparticle domain deactivation. The data-mining approach described in this work is widely applicable to many other structurally complex and chemically heterogeneous systems, in which the secondary/minority phases could critically affect the overall performance of the system, well beyond battery research.