RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var.
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 flavo...
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e34.pdf |
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| author | Neha Samir Roy Jung-A Kim Ah-Young Choi Yong-Wook Ban Nam-Il Park Kyong-Cheul Park Hee-sun Yang Ik-Young Choi Soonok Kim |
| author_facet | Neha Samir Roy Jung-A Kim Ah-Young Choi Yong-Wook Ban Nam-Il Park Kyong-Cheul Park Hee-sun Yang Ik-Young Choi Soonok Kim |
| author_sort | Neha Samir Roy |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8866513f6100477ca043cdfb1847597b |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-8866513f6100477ca043cdfb1847597b2025-02-02T03:21:17ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e34536RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var.Neha Samir Roy0Jung-A Kim1Ah-Young Choi2Yong-Wook Ban3Nam-Il Park4Kyong-Cheul Park5Hee-sun Yang6Ik-Young Choi7Soonok Kim8 Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea DNACare Genomics Institute, Seongnam 13558, Korea Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea Department of Plant Science, Gangneung Wonju National University, Gangneung 25457, Korea Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, KoreaCirsium 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.http://genominfo.org/upload/pdf/gi-2018-16-4-e34.pdf differentially expressed geneRNA-sequencingsilymarintranscriptome |
| spellingShingle | Neha Samir Roy Jung-A Kim Ah-Young Choi Yong-Wook Ban Nam-Il Park Kyong-Cheul Park Hee-sun Yang Ik-Young Choi Soonok Kim RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. Genomics & Informatics differentially expressed gene RNA-sequencing silymarin transcriptome |
| title | RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. |
| title_full | RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. |
| title_fullStr | RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. |
| title_full_unstemmed | RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. |
| title_short | RNA-Seq Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb var. |
| title_sort | rna seq assembly and differential transcriptome analysis of korean medicinal herb var |
| topic | differentially expressed gene RNA-sequencing silymarin transcriptome |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e34.pdf |
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