Abstract
Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.
Highlights
Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, is native to China and has been widely used in Traditional Chinese Medicine (TCM) for centuries (Kamath, Skeels & Pai, 2009; Xiang et al, 2016)
We further used a core eukaryotic gene mapping approach [CEGMA (Parra, Bradnam & Korf, 2007)] to identify the core genes in the Chinese goldthread transcripts and unigenes; and more than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively (Table 2)
Chemical analyses of the rhizome indicated that berberine is the most abundant, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions
Summary
Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, is native to China and has been widely used in Traditional Chinese Medicine (TCM) for centuries (Kamath, Skeels & Pai, 2009; Xiang et al, 2016). The distribution of the Chinese goldthread is limited to narrow regions west of China, such as Chongqing, Shaanxi and Guizhou province, due to variants of climate, topography and other environmental factors, the chemical composition of the alkaloids and the quantity of each alkaloids component in different biotope is different, resulting in different drug efficacy (Geng et al, 2010)
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