Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Xu, Haibin; Song, Jingyuan; Luo, Hongmei; Zhang, Yujun; Li, Qiushi; Zhu, Yingjie; Xu, Jiang; Lü, Ying; Song, Chi; Wang, Bo; Sun, Wei; Shen, Guoan; Zhang, Xin; Qian, Jun; Ji, Aijia; Xu, Zhichao; Luo, Xiang; He, Li; Li, Chuyuan; Sun, Chao; Yan, Hu; Cui, Guanghong; Li, Xiwen; Li, Xianen; Wei, Jianhe; Liu, Juyan; Wang, Ying; Hayward, Alice; Nelson, David R.; Ning, Zemin; Peters, Reuben J.; Qi, Xiaoquan; Chen, Shilin

doi:10.1016/j.molp.2016.03.010

Cited by 260 publications

(225 citation statements)

References 12 publications

(20 reference statements)

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“…To obtain sequencing data for all of the SmPPO genes, tBLASTn searches were performed on the genome database of S. miltiorrhiza line 99-3 (http://www.ndctcm.org/)28. An e-value cut-off of e −10 was applied.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Jiang

et al. 2017

Sci Rep

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Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.

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Section: Methodsmentioning

confidence: 99%

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Jiang

et al. 2017

Sci Rep

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“…Whole-genome sequencing has become a practical strategy to identify metabolic pathways for natural product biosynthesis (Liu et al, 2017;Mochida et al, 2017), and genome sequences of members of the order Lamiales such as Salvia miltiorrhiza (Zhang et al, 2015;Xu et al, 2016), Salvia splendens (Dong et al, 2018), and Sesamum indicum (Zhang et al, 2013) make feasible the comparative analysis to investigate how RSFs are produced in Scutellaria.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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.

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“…The S. barbata genome identified 93.0% of complete BUSCO gene models and had a 95.0% DNA mapping rate. The high-quality genome assemblies of S. baicalensis and S. barbata showed the great advantage of single molecule sequencing, with assembly metrics that were far better than those of other reported genomes of Lamiaceae species, i.e., Salvia miltiorrhiza [28] and Mentha longifolia [29].…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis ofScutellaria baicalensisandScutellaria barbataReveals the Evolution of Active Flavonoid Biosynthesis

Gao

et al. 2020

Preprint

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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...

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Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Cited by 260 publications

References 12 publications

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza

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

Comparative Genome Analysis ofScutellaria baicalensisandScutellaria barbataReveals the Evolution of Active Flavonoid Biosynthesis

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