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DOI: 10.1055/a-1209-3407
Comparative Transcriptome Analysis Reveals Candidate Genes Involved in Isoquinoline Alkaloid Biosynthesis in Stephania tetrandra
Abstract
The roots of Stephania tetrandra are used as a traditional Chinese medicine. Isoquinoline alkaloids are considered to be the most important and effective components in this herb, but little is known about the molecular mechanism underlying their biosynthesis. In this context, this study aimed to reveal candidate genes related to isoquinoline alkaloid biosynthesis in S. tetrandra. Determination of tetrandrine and fangchinoline in the roots and leaves of S. tetrandra by HPLC showed that the roots had much higher contents of the two isoquinoline alkaloids than the leaves. Thus, a comparative transcriptome analysis of the two tissues was performed to uncover candidate genes involved in isoquinoline alkaloid biosynthesis. A total of 71 674 unigenes was obtained and 31 994 of these were assigned putative functions based on BLAST searches against 6 annotation databases. Among the 79 isoquinoline alkaloid-related unigenes, 51 were differentially expressed, with 42 and 9 genes upregulated and downregulated, respectively, when the roots were compared with the leaves. The upregulated differentially expressed genes were consistent with isoquinoline alkaloid accumulation in roots and thus were deemed key candidate genes for isoquinoline alkaloid biosynthesis in the roots. Moreover, the expression profiles of 10 isoquinoline alkaloid-related differentially expressed genes between roots and leaves were validated by quantitative real-time polymerase chain reaction, which indicated that our transcriptome and gene expression profiles were reliable. This study not only provides a valuable genomic resource for S. tetrandra but also proposes candidate genes involved in isoquinoline alkaloid biosynthesis and transcription factors related to the regulation of isoquinoline alkaloid biosynthesis. The results lay a foundation for further studies on isoquinoline alkaloid biosynthesis in this medicinal plant.
Key words
Menispermaceae - Stephania tetrandra - transcriptome - isoquinoline alkaloids - biosynthesis - RT-qPCRSupporting Information
- Supporting Information
Retention times, regression equations, correlation coefficients, LODs, LOQs, linear ranges, precision, accuracy, and repeatability for the two analytes in S. tetrandra (Tables 1S and 2S, respectively), the contents of the two analytes in the three batches of S. tetrandra (Table 3S), KEGG pathways assigned to the unigenes, 79 unigenes related to isoquinoline alkaloid biosynthesis, 15 DEGs encoding WRKY TFs, and 30 DEGs encoding bHLH TFs in S. tetrandra (Tables 4S–6S, respectively), primer sequences used in qRT-PCR (Table 7S), length distribution of S. tetrandra unigenes (Fig. 1S), classification of the S. tetrandra unigenes based on GO and COG analysis (Figs. 2S and 3S, respectively), unigenes expressed in the leaves and roots of S. tetrandra (Fig. 4S), and GO enrichment analysis of the DEGs and heat map based on the expression level of the IQA-related DEGs between the roots and leaves of S. tetrandra (Figs. 5S and 6S, respectively) are available as Supporting Information.
Publication History
Received: 07 February 2020
Accepted after revision: 21 June 2020
Article published online:
05 August 2020
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