Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes

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.

Identification and Characterization of Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in Coptis Species

“…According to previous reports, berberine, coptisine, jatrorrhizine, and palmatine constitute the main BIAs of C. teeta and C. chinensis ( Kamath et al, 2009 ; Chen et al, 2017 ; Yang et al, 2017 ). HPLC analysis of leaves, roots, and rhizomes of C. teeta and C. chinensis indicated the presence of berberine, coptisine, jatrorrhizine, and palmatine in both species ( Figure 3 ).…”

“…The enzymes encoded by the genes NCS, 6OMT , and 4 ′ OMT are located upstream of the BIA synthetic pathway from a key branch-point intermediate ( S )-reticuline, whereas SOMT is involved in the synthesis of berberine and palmatine. The differential gene expression patterns of two Coptis species may have resulted from their growth environment, climate, topography, other environmental factors, and cultivation conditions ( Chen et al, 2017 ). Moreover, these results coincided with the higher contents of major BIAs in the roots of the two Coptis species ( Figure 3 ).…”

“…The major active components in C. chinensis are benzylisoquinoline alkaloids (BIAs) ( Kamath et al, 2009 ; Chen et al, 2017 ). Of great interest in this field are the identification of effective separation methods and assessment of their efficacy in the treatment of various diseases ( Tjong et al, 2011 ; Zhang et al, 2011 ; Cui et al, 2016 ; Friedemann et al, 2016 ; Kim et al, 2016 ).…”

“…With the rapid development of RNA sequencing technology, it is easy to capture the candidate genes at a genome-wide scale. In a recent study, Chen et al (2017) analyzed major components of C . chinensis from three biotopes; namely, Zhenping, Zunyi, and Shizhu, and found that berberine was highest in concentration, followed sequentially by coptisine, palmatine, and epiberberine in all three accessions.…”

Gloriosa superba and Colchicum autumnale multi-tissue transcriptome analysis for colchicine pathway and rhizome development candidate gene identification

“…Transcription factor families such as AP2-EREBP, bHLH, MYB, NAC, and WRKY were reported to be important in regulating specialized metabolic pathways in rhizomes [61]. Bioactive small molecules such as curcuminoid and candidate genes for gingerol synthesis are also highly expressed in rhizomes [67][68][69][70][71]. Notably, biosynthetic genes involved in benzylisoquinoline alkaloid formation were highly upregulated during bulb development in Corydalis yanhusuo [72].…”