Genomics Inform.  2018 Dec;16(4):e34. 10.5808/GI.2018.16.4.e34.

RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum

Affiliations
  • 1Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea. choii@kangwon.ac.kr
  • 2Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea.
  • 3Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea. sokim90@korea.kr
  • 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.

Abstract

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.

Keyword

Cirsium japonicum; differentially expressed gene; RNA-sequencing; silymarin; transcriptome

MeSH Terms

Asia
Asteraceae
Cirsium*
Dataset
Estrone
Flavones
Flowers
Gene Expression Profiling*
Genetic Engineering
Genomics
Humans
Plants, Medicinal*
Sequence Analysis, RNA
Silymarin
Transcriptome*
Estrone
Flavones
Silymarin
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