The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

Abstract

Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, ''Huang Qin,'' are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4 0 -deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4 0 -deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo-and subfunctionalizations were involved in the evolution of 4 0 -deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.

RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

“…The phylogenetic analysis of the transcriptomes of the 13 berry fruit species together with the genome sequences of seven reference species ( A. thaliana [109], P. trichocarpa [110], G. max [111], V. vinifera [5], S. lycopersicum [112], O. sativa [113] and A. trichopoda [114]) was carried out following the comparative genomic analysis detailed in [115]. EvidentialGene [116] was used to translate and validate the ORFs.…”

Applications, phytochemistry, pharmacological effects, pharmacokinetics, toxicity of Scutellaria baicalensis Georgi. and its probably potential therapeutic effects on COVID-19: a review

“…There are more than 100 kinds of flavonoids in SB, it is important to note that pharmacological activities of SB take place due to the presence of specific 4′-deoxyflavones such as chrysin, baicalein, wogonin and their glycosides (baicalin and wogonoside) [ 41 ]. The key enzymes for the synthesis of these compounds are mainly found in roots, including PAL, C4H, CLL, CHS, CHI, FNSII, MT, GT, FH and OMT, different flavonoid synthetases are encoded by different genes [ 6 , 42 , 43 ]. The main synthetic routes of flavonoids were shown in Fig.…”

“…SB has antibacterial, antiviral, anti-inflammatory, anticancer, liver and nerve protective functions, etc. [ 6 – 8 ]. Because SB has a very wide range of pharmacological effects and clinical applications, more and more in-depth researches had been implemented.…”

Chromosome Level Genome Assembly of Andrographis paniculata

“…Particularly, genome sequencing is a powerful tool for studying various aspects of physiology and genetics in non-model plants, many of which are traditional herbal plants ( Zerikly and Challis, 2009 ; De Luca et al, 2012 ; Chae et al, 2014 ). For example, the reference genome of Scutellaria baicalensis ( Zerikly and Challis, 2009 ; De Luca et al, 2012 ; Chae et al, 2014 ; Zhao et al, 2019 ), Panax ginseng ( Xu et al, 2017 ), mint ( Vining et al, 2017 ), and opium poppy ( Guo et al, 2018 ) provided insights into the genes involved in the biosynthesis of unique flavonoids, terpenes, alkaloids and many other secondary metabolites. Additionally, the reference genome of Salvia splendens was very valuable for helping marker-assisted breeding, genome editing, and molecular genetics ( Dong et al, 2018 ).…”