Deep Sequencing of the Scutellaria baicalensis Georgi Transcriptome Reveals Flavonoid Biosynthetic Profiling and Organ-Specific Gene Expression.

Jinxin Liu,Linchun Shi,Heng Lu,Fanyun Meng,Geng Li,Jingyi Hou,Chao Jiang,Mukesh Jain

doi:10.1371/journal.pone.0136397

Abstract

Scutellaria baicalensis Georgi has long been used in traditional medicine to treat various such widely varying diseases and has been listed in the Chinese Pharmacopeia, the Japanese Pharmacopeia, the Korean Pharmacopoeia and the European Pharmacopoeia. Flavonoids, especially wogonin, wogonoside, baicalin, and baicalein, are its main functional ingredients with various pharmacological activities. Although pharmaological studies for these flavonoid components have been well conducted, the molecular mechanism of their biosynthesis remains unclear in S. baicalensis. In this study, Illumina/Solexa deep sequencing generated more than 91 million paired-end reads and 49,507 unigenes from S. baicalensis roots, stems, leaves and flowers. More than 70% unigenes were annotated in at least one of the five public databases and 13,627 unigenes were assigned to 3,810 KEGG genes involved in 579 different pathways. 54 unigenes that encode 12 key enzymes involved in the pathway of flavonoid biosynthesis were discovered. One baicalinase and three baicalein 7-O-glucuronosyltransferases genes potentially involved in the transformation between baicalin/wogonoside and baicalein/wogonin were identified. Four candidate 6-hydroxylase genes for the formation of baicalin/baicalein and one candidate 8-O-methyltransferase gene for the biosynthesis of wogonoside/wogonin were also recognized. Our results further support the conclusion that, in S. baicalensis, 3,5,7-trihydroxyflavone was the precursor of the four above compounds. Then, the differential expression models and simple sequence repeats associated with these genes were carefully analyzed. All of these results not only enrich the gene resource but also benefit research into the molecular genetics and functional genomics in S. baicalensis.

Highlights

Scutellaria baicalensis Georgi (Baikal skullcap or Huang-Qin in Chinese), belonging to the Lamiaceae family, is widely used in traditional medicine and has been listed in the Chinese Pharmacopeia [1], the Japanese Pharmacopeia [2], the Korean Pharmacopoeia [3] and the European Pharmacopoeia [4]
Our results proposed that RNA sequencing (RNA-seq) could be an ideal method to obtain insights into the complex transcriptome of S. baicalensis, and these transcriptome datasets will provide a valuable resource for research on the regulation of flavonoid biosynthesis
The S. baicalensis natural flavonoids, especially their glycosides have diverse biological activities and S. baicalensis has been proposed as an excellent model system for continued research of useful medicinal compounds[64]

Summary

Introduction

Scutellaria baicalensis Georgi (Baikal skullcap or Huang-Qin in Chinese), belonging to the Lamiaceae family, is widely used in traditional medicine and has been listed in the Chinese Pharmacopeia [1], the Japanese Pharmacopeia [2], the Korean Pharmacopoeia [3] and the European Pharmacopoeia [4]. Baicalein, wogonoside and wogonin are the main flavonoid components in S. baicalensis, and have various pharmacological activities, such as antitumor effects, antioxidative action, anti-inflammatory, antibacterial and antiviral activities [6,7,8]. Baicalin and wogonoside can be hydrolyzed into baicalein and wogonin directly [10]. The amount of total baicalein component in roots of S. baicalensis is far higher than that in the aboveground parts including stems, leaves and flowers. With the dramatically increasing utilization of S. baicalensis for medicine in recent years, the wild resource of the plant is too limited to satisfy demand

Methods

Results

Conclusion