Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

Abstract

39 Scutellaria baicalensis and Scutellaria barbata, common medicinal plants of the 40 Lamiaceae family, produce specific flavonoid compounds with antioxidant and 41 antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their 42 glycosides. Here, we reported two chromosome-level genome assemblies of S. 43 baicalensis and S. barbata with significant quantitative chromosomal variation (2n = 44 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred 45 far earlier than previously reported, and a whole-genome duplication event was 46 identified. The insertion of long terminal repeat elements after speciation might be 47 responsible for the observed chromosomal expansion and rearrangement. The 48 comparative genome analysis of congeneric species elucidated the species-specific 49 evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific 50 tandem duplication of the phenylalanine ammonia lyase (PAL) and chalcone synthase 51 (CHS) genes, and the S. barbata-specific duplication of 4-CoA ligase (4CL) genes. In 52 addition, the paralogous duplication, collinearity, and expression diversity of CYP82D 53 subfamily members revealed the functional divergence of flavone hydroxylase genes 54 between S. baicalensis and S. barbata. These Scutellaria genomes highlight the 55 common and species-specific evolution of flavone biosynthetic genes, promoting the 56 development of molecular breeding and the study of the biosynthesis and regulation of 57 bioactive compounds.58 59 KEYWORDS: Scutellaria; comparative genome; flavonoid biosynthesis; tandem 60 duplication; species-specific evolution 61 62 63 65 proanthocyanidins, and isoflavones, play important functions in plants, such as flower 66 pigmentation, UV protection, and symbiotic nitrogen fixation [1−3]. Flavonoid 67 metabolites also have biological and pharmacological activities in human health, 68 including antibacterial and antioxidant functions, and the treatment of cancer, 69 inflammatory, and cardiovascular diseases [3]. The genus Scutellaria, belong to the 70 Lamiaceae family, comprises common herbal plants enriched by bioactive flavonoids, 71 and approximately 300 to 360 Scutellaria species have been documented as having the 72 characteristic flower form of upper and lower lips [4,5]. Only two Scutellaria species, 73 Scutellaria baicalensis and Scutellaria barbata, are recorded in the Chinese 74 pharmacopoeia, and the roots of S. baicalensis and dried herbs of S. barbata are the 75 basis of the Chinese medicines Huang Qin and Ban Zhi Lian, respectively, which have 76 been well known heat-clearing and detoxifying herbs for thousands of years [6]. The 77 main biologically active compounds in Scutellaria are derivatives of chrysin and 78 apigenin, such as baicalein, scutellarein, wogonin, and their glycosides (baicalin, 79 scutellarin, and wogonoside) [7−10]. Baicalin has been confirmed to activate carnitine 80 palmitoyltransferase 1 in the treatment of diet-induced obesity and hepatic st...

<strong>SMARTdenov</strong><strong>o: A <em>de novo</em> Assembler Using Long Noisy Reads</strong>

“…SMARTdenovo has been available since 2015 on github, but its performance not only remains comparable with current assemblers, and but also has several advantages as described. Furthermore, given its excellent performance for use on corrected long sequence reads, it continues to be widely used in for genome assembly projects today [33][34][35][36][37][38][39][40][41][42].…”

SMARTdenovo: a de novo assembler using long noisy reads

“…Furthermore, given its excellent performance for use on corrected long sequence reads, it continues to be widely used in for genome assembly projects today [34][35][36][37][38][39][40][41][42][43].…”

Research progress in biosynthesis and synthetic biology of active ingredients of &lt;italic&gt;Scutellaria baicalensis&lt;/italic&gt; Georgi based on multi-omics approach

“…与大 多数植物一样, 黄芩叶绿体基因组也是由两个保守的 反向重复(inverted repeat, IR)区域(IRA和IRB)分成的 环状四分体结构. 为了研究黄芩道地性物质基础, 阐 释黄芩的分子谱系地理学, Jiang等人 [28] 利用shortrange PCR方法分别对来自黑龙江省和山西省的两个 黄芩个体叶绿体基因组进行测序, 组装出叶绿体基因 组大小分别为151817 bp和151824 bp, GC含量为 图 2 黄芩与半枝莲基因组染色体共线性及物种分化时间分析 [25] . A: 黄芩根及地上部分的形态; B: 黄芩和半枝莲基因组共线 性分析; C: 基于黄芩等基因组的物种进化及全基因组复制事件(网络版彩图)…”