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Due to the lack of a Panax japonicus var. major reference genome, we assembled a reference transcriptome from P. japonicus C. A. Mey transcriptome sequencing data, and 203 283 unigenes were obtained. In this study, with the assistance from the Trinity, Bowtie2 and SAMtools softwares, 218 465 single nucleotide polymorphisms (SNPs) were identified by mapping the Illumina sequences to the reference transcriptome. The SNP forms included 126 262 transformations and 92 203 transversions. A large number of SNP loci were associated with triterpenoid saponin synthesis: 54 SNPs were associated with cytochrome P450, one with glycosyl transferase and 94 with the biosynthesis of the triterpenoid saponin backbone.

SNP discovery and functional annotation in the Panax japonicus var. major transcriptome