De novo transcriptome assembly and the identification of gene-associated single-nucleotide polymorphism markers in Asian and American ginseng roots

Abstract

We performed de novo transcriptome sequencing for Panax ginseng and Panax quinquefolius accessions using the 454 GS FLX Titanium System and discovered annotation-based genome-wide single-nucleotide polymorphism (SNPs) using next-generation ginseng transcriptome data without reference genome sequence. The comprehensive transcriptome characterization with the mature roots of four ginseng accessions generated 297,170 reads for 'Cheonryang' cultivar, 305,673 reads for 'Yunpoong' cultivar, 311,861 reads for the G03080 breeding line, and 308,313 reads for P. quinquefolius. In transcriptome assembly, the lengths of the sample read were 156.42 Mb for 'Cheonryang', 161.95 Mb for 'Yunpoong', 165.07 Mb for G03080 breeding line, and 166.48 Mb for P. quinquefolius. A total of 97 primer pairs were designed with the homozygous SNP presented in all four accessions. SNP genotyping using high-resolution melting (HRM) analysis was performed to validate the putative SNP markers of 97 primer pairs. Out of the 73 primer pairs, 73 primer pairs amplified the target sequence and 34 primer pairs showed polymorphic melting curves in samples from 11 P. ginseng cultivars and one P. quinquefolius accession. Among the 34 polymorphic HRM-SNP primers, four primers were useful to distinguish ginseng cultivars. In the present study, we demonstrated that de novo transcriptome assembly and mapping analyses are useful in providing four HRM-SNP primer pairs that reliably show a high degree of polymorphism among ginseng cultivars.

Applications of molecular markers in the discrimination of Panax species and Korean ginseng cultivars ( Panax ginseng )

“…It is now possible to elucidate a large number of SNPs using transcript information. Consistent with this trend, Jo et al [54] identified a large number of SNPs in the transcript information on ginseng and developed high-resolution melting (HRM) analysis that can distinguish cultivars ( Fig. 4 ).…”

“…4 Examples of rapid discrimination of Panax ginseng cultivars and Panax quinquefolius by use of high-resolution melt analysis with (A) GHP 01095, (B) GHP 11494, (C) GHP 13830, and (D) GHP 15673 markers. Temperature unit is °C (Jo et al [54] , 2015). …”

Comparative transcriptome analyses on terpenoids metabolism in field- and mountain-cultivated ginseng roots

“…Since Kim et al [19] reported the first transcriptome from the leaf of ginseng, comparative transcriptome analyses have also been widely conducted on different ginseng roots, such as roots of two Korean ginseng cultivars (i.e., cultivars Cheonryang and Yunpoong ) and American ginseng ( P. quinquefolius , Voucher no. MPS002310) [20], adventitious roots from five Korean ginseng cultivars (i.e., cultivars Chunpoong , Cheongsun , Sunhyang , Goopong , and Sunun ) [21], or four parts of the root of the Korean ginseng cultivar Chunpoong (i.e., whole root, main root body, rhizome, and lateral root) [22], providing new insights into the primary and secondary metabolisms of ginseng root. Specific to comparative transcriptome analyses of FCG and MCG roots, several key genes in terpenoids biosynthesis have been reported.…”

Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome

“…In particular, transcriptome profile studies (primarily of roots) in P. ginseng and close relatives have provided genomic resources to identify candidate genes associated with traits such as triterpenoid saponin biosynthesis [ 12 , 13 ]. However, transcripts produced with the Illumina Hi-seq platform were short, incomplete and provided limited DNA structural information [ 14 , 15 ]. With genomic information, genomic resources such as molecular markers, genome assembly and transcriptome data can be developed to improve crop breeding and other applications of P. ginseng research [ 16 , 17 ].…”