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Genomics Inform > Volume 16(4); 2018 > Article
DOI:    Published online December 28, 2018.
RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum
Neha Samir Roy1,2, Jung-A Kim3, Ah-Young Choi4, Yong-Wook Ban5, Nam-Il Park6, Kyong-Cheul Park1, Hee-sun Yang3, Ik-Young Choi1,2, Soonok Kim3
1Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
2Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
3Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
4DNACare Genomics Institute, Seongnam 13558, Korea
5Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
6Department of Plant Science, Gangneung Wonju National University, Gangneung 25457, Korea
Corresponding author:  Ik-Young Choi
Tel: +82-33-250-7768   Email:
Soonok Kim
Tel: +82-32-590-7110   Email:
Received: December 10, 2018   Revised: December 17, 2018   Accepted: December 17, 2018
Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.
Keywords: Cirsium japonicum, differentially expressed gene, RNA-sequencing, silymarin, transcriptome
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