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Updated: Sep 24, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
SNP discovery and functional annotation in the Panax japonicus var. major transcriptome
Jian Li1, Ding-Ping Bai1, Xi-Feng Zhang2
1Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University Fuzhou 350002 China.
Abstract:
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.
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