Structural Variation, Functional Differentiation, and Activity Correlation of the Cytochrome P450 Gene Superfamily Revealed in Ginseng

Ginseng (Panax ginseng C. A. Mey.) is one of the most important medicinal herbs for human health and medicine, for which ginsenosides are the major bioactive components. The cytochrome P450 genes, CYP, form a large gene superfamily; however, only three CYP genes have been identified from ginseng and shown to be involved in ginsenoside biosynthesis, indicating the importance of the CYP gene superfamily in the process. Here we report genome-wide identification and systems analysis of the CYP genes in ginseng, defined as PgCYP genes. We identified 414 PgCYP genes, including the three published PgCYP genes. These PgCYP genes formed a superfamily consisting of 41 gene families, with a substantial diversity in phylogeny and dramatic variation in spatiotemporal expression. Gene ontology (GO) analysis categorized the PgCYP gene superfamily into 12 functional subcategories distributing among all three primary functional categories, suggesting its functional differentiation. Nevertheless, the majority of its gene members expressed correlatively and tended to form a coexpression network and some of them were commonly regulated in expression across tissues and developmental stages. These results have led to genome-wide identification of PgCYP genes useful for genome-wide identification of the PgCYP genes involved in ginsenoside biosynthesis in ginseng and provided the first insight into how a gene superfamily functionally differentiates and acts correlatively in plants.