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. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred 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 evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of 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 CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes 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.
新型冠状病毒肺炎（COVID-19）肆虐全球，中医药在新冠诊治方面发挥积极作用。中药黄芩和半枝莲具有清热解毒功效，其基原植物为唇形科黄芩属植物黄芩（Scutellaria baicalensis）和半枝莲（Scutellaria barbata），主要活性成分为黄酮类化合物，如黄芩素、汉黄芩素、野黄芩素及其糖苷类化合物。黄芩活性成分的生物合成途径及体外合成生物学研究受国际关注。本研究报道了黄芩和半枝莲的染色体水平基因组序列。通过单拷贝基因构建系统发育树揭示黄芩和半枝莲的分化时间（13.28MYA）远早于之前的报道（3.35MYA），基于同源基因的同义替换速率研究发现唇形科与胡麻科共享的全基因组复制（WGD）事件。半枝莲基因组中长末端重复序列的近期插入可能与其染色体的重排和扩张相关。比较基因组研究显示芹菜素和白杨素合成途径相关基因在黄芩和半枝莲中特异性的扩张，如黄芩特异的苯丙氨酸解氨酶（phenylalanine ammonia-lyase，PAL）和查尔酮合成酶（chalcone synthase，CHS）编码基因的串联复制，以及半枝莲特异的4-香豆酰辅酶A连接酶（4-coumarate CoA ligase, 4CL）的扩张。此外，基于基因组共线性及不同组织部位基因表达研究发现黄芩和半枝莲中黄酮羟化酶编码基因（CYP82Ds）的复制及功能差异。本研究将有助于理解黄芩和半枝莲黄酮类化合物的合成及进化机制，为中药黄芩和半枝莲的高品质分子辅助育种等研究奠定基础。





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