Comparative Genome Analysis of Scutellaria Baicalensisand Scutellaria BarbataReveals the Evolution of Active Flavonoid Biosynthesis

Scutellaria baicalensis(S. baicalensis) and Scutellaria barbata(S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensisand S. barbatawith quantitative chromosomal variation (2n= 18 and 2n= 26, respectively). The divergence of S. baicalensisand S. barbataoccurred far earlier than previously reported, and a whole-genome duplication(WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolutionof chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplicationof genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82Dsubfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensisand S. barbata. Analyzing these Scutellariagenomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.