Transcriptome Profiling and Comparative Analysis of Panax ginseng Adventitious Roots

Abstract

Panax ginseng (C. A. Meyer) is a traditional medicinal plant famous for its strong therapeutic effects. However, genomic resources for P. ginseng are still very limited. In this study, we performed de novo assembly of transcriptomes from adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS). The assemblies were generated from ~85 and ~77 million high-quality Illumina HiSeq 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 TAIR databases. We identified candidate genes involved in ginsenoside biosynthesis: 10 transcripts for farnesyl diphosphate synthase to protopanaxatriol synthase and 21 transcripts for UDP-glycosyltransferase. A large number of transcripts (17%) with different GO designations were uniquely detected in adventitious roots compared to normal ginseng roots. In addition, 10,213 and 7,928 cDNA SSRs were identified as potential molecular markers in CP and CS, respectively. Our assembly of ginseng transcriptomes demonstrates the successful application of genomics approaches to large complex genomes. In addition, we have predicted the long noncoding(lncRNA) based on our CP RNA-Seq data. A total of 11,270 lncRNA were identified. Among them, some were precursors of small RNAs such as microRNAs and siRNAs. The assembly and comparative analysis data have been deposited to our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. Further, To better understand our ginseng genome (P. ginseng), we used Chunpoong (CP) adventitious root RNA-Seq data to identify lncRNAs of P. gisneng. we found 11,270 long noncoding RNAs which had multiexonic structures. A total of 433 lncRNAs showed significant similarity against publicly available lncRNA database of Arabidopsis, Maize, lncRNA database and Rfam. My study provides a preliminary source for future studies of lncRNA content and function in ginseng.