Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei.
BACKGROUND
Valeriana 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.


RESULTS
A 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.


CONCLUSIONS
We 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.
Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Korea.
Yun Ji
YJ
Park
Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Korea.
Xiaohua
X
Li
Code Division, Insilicogen Inc., Suwon, Gyeonggi-do, 441-813, Korea.
Seung Jae
SJ
Noh
Division of Life Sciences and Bio-Resource and Environmental Center, Incheon National University, Yeonsu-gu, Incheon, 406-772, Korea.
Jae Kwang
JK
Kim
Department of Food and Nutrition and Institute of Natural Medicine, Hallym University, Chuncheon, 200-702, Korea.
Soon Sung
SS
Lim
Deptartment of Plant Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do, 210-702, Korea.
Nam Il
NI
Park
Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Korea.
Soonok
S
Kim
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk, 369-873, Republic of Korea.
Yeon Bok
YB
Kim
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk, 369-873, Republic of Korea.
Young Ock
YO
Kim
Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Bisanro 92, Eumseong, Chungbuk, 369-873, Republic of Korea.
Sang Won
SW
Lee
Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia.
Mariadhas Valan
MV
Arasu
Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia.
Naif Abdullah
NA
Al-Dhabi
Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Korea. supark@cnu.ac.kr.
Sang Un
SU
Park
D002338:Carotenoids / Q000096:biosynthesis; D002851:Chromatography, High Pressure Liquid; D008401:Gas Chromatography-Mass Spectrometry; D059014:High-Throughput Nucleotide Sequencing; D055442:Metabolome; D018517:Plant Roots / Q000235:genetics; D018520:Plant Shoots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D064210:Secondary Metabolism / Q000235:genetics; D017423:Sequence Analysis, RNA; D013729:Terpenes / Q000378:metabolism; D059467:Transcriptome; D014632:Valerian / Q000235:genetics*
D018749:RNA, Plant; D013729:Terpenes; D002338:Carotenoids
Carotenoid; Digital gene expression; Illumina HiSeq system; Phenylpropanoid; Terpenoid; Valeriana fauriei