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BMC Genomics

, 17:303

Transcriptomic methods

Abstract

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.

KeywordsValeriana fauriei Illumina HiSeq system Digital gene expression Terpenoid Carotenoid Phenylpropanoid Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-2616-3 contains supplementary material, which is available to authorized users.

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Autor: Yun Ji Park - Xiaohua Li - Seung Jae Noh - Jae Kwang Kim - Soon Sung Lim - Nam Il Park - Soonok Kim - Yeon Bok Kim -

Fuente: https://link.springer.com/







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