Comparative genomics of three medicinal Glycyrrhiza species unveiled novel candidates for the production of important bioactive compounds

Licorice is a popular herb around the world, with Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra being the three most common medicinal species. Glycyrrhizin, the most important bioactive compound, determines the quality of medicinal licorices. Besides, some characteristic flavonoids, such as licochalcone A (LCA) from G. inflata and glabridin from G. glabra, are emerging as expensive raw materials in the fields of medicine and cosmetics. We obtained high-quality genomic sequence data of these three licorices with sizes of 425, 447, and 423 Mb, respectively. By genome assembly-assisted comparison, collinear relationships and structural variations (SVs) among the three Glycyrrhiza species were identified. These presence/absence variations (PAV) genes were mainly enriched in secondary metabolism pathways. With the assembled genomes and transcriptomes, we constructed the regulatory network of glycyrrhizin in G. inflata and identified GibHLH9, GibHLH53, and GibHLH174 as key transcription factors that promote glycyrrhizin by transactivating the expression of GiCSyGT and GiUGT73P12, respectively. In addition, genes in the proposed LCA and glabridin biosynthesis pathways were analyzed and identified from all three genomes. Then the function of GiOMT17 in the biosynthesis of LCA was confirmed in vivo and in vitro. As a consequence, the appearance of unique genes and differential expression of commonly existed genes explains why all three medicinal licorice species synthesize these characteristic flavonoids but only specific species accumulate them to a certain amount. Our findings provide high-quality genomes for future research of Glycyrrhiza and supply valuable gene resources for synthetic biology and molecular breeding for high-yield active ingredients.