Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei

BMC Genomics

Research Article

Soonok Kim¹  Seung Jae Noh²  Naif Abdullah Al-Dhabi³  Mariadhas Valan Arasu³  Yun Ji Park⁴  Xiaohua Li⁴  Sang Un Park⁴  Soon Sung Lim⁵  Sang Won Lee⁶  Young Ock Kim⁶  Yeon Bok Kim⁶  Nam Il Park⁷  Jae Kwang Kim⁸ 

[1] Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 404-170, Incheon, Korea;Code Division, Insilicogen Inc., 441-813, Suwon, Gyeonggi-do, Korea;Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, 11451, Riyadh, Saudi Arabia;Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, 305-764, Daejeon, Korea;Department of Food and Nutrition and Institute of Natural Medicine, Hallym University, 200-702, Chuncheon, Korea;Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, 369-873, Eumseong, Chungbuk, Republic of Korea;Deptartment of Plant Science, Gangneung-Wonju National University, 7 Jukheon-gil, 210-702, Gangneung-si, Gangwon-do, Korea;Division of Life Sciences and Bio-Resource and Environmental Center, Incheon National University, Yeonsu-gu, 406-772, Incheon, Korea;

关键词: Valeriana fauriei;    Illumina HiSeq system;    Digital gene expression;    Terpenoid;    Carotenoid;    Phenylpropanoid;   

DOI  :  10.1186/s12864-016-2616-3

 received in 2015-08-11, accepted in 2016-04-13,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundValeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei.ResultsA total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei.ConclusionsWe have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid.

【 授权许可】

CC BY   
© Park et al. 2016