Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

Abstract

BackgroundPanax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential.MethodsRNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed.ResultsAssemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots.ConclusionThis study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments

“…The average transcript length was 1002.5 bp, and the N50 was 1439 bp. These parameters were both far longer than those of most similar ginseng studies (Table 2) [16][17][18][19]. The ginsenosides content [16] P. quinquefolius [17] P. ginseng [18] P. ginseng [19] P *, This assembly consists of 86,609 contigs and 91,536 singletons, which have a length range of 100-7,858 and 100-691, respectively.…”

A simple real-time polymerase chain reaction (PCR)-based assay for authentication of the Chinese Panax ginseng cultivar Damaya from a local ginseng population

“…Nowadays, a large amount of sequences are obtained by genomic and transcriptomic sequencing (Sathiyamoorthy et al, 2010;Li et al, 2013;Jayakodi et al, 2014), but development of cultivar-specific marker is still difficult as these sequences are usually generated from a single specific cultivar. Thus, it is not feasible to exploit SNPs by multiple alignments of redundant EST sequences.…”

Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars

“…Adventitious roots were induced and cultivated in bioreactors as previously described [20]. Adventitious roots maintained in bioreactors were transferred into 250-mL flasks containing 100 mL Schenk and Hildebrandt liquid medium [21] supplemented with 3 mg/L indole-3-butyric acid (IBA) and 5% sucrose and cultured at 25°C on a rotary shaker under dark conditions.…”

“…The raw RNA-seq data from CS and SH were deposited in the NCBI Sequence Read Archive (SRA, http://www.ncbi.nlm.nih.gov/Traces/sra) under accession numbers SRR1688723 and SRR1688724, respectively. The raw RNA-seq data from CP were obtained from our previous report [20] (Accession number: SRR619718). Adapter sequences and low-quality bases were filtered using NGS QC Toolkit [22].…”