Comprehensive comparative analysis of chloroplast genomes from seven Panax species and development of an authentication system based on species-unique single nucleotide polymorphism markers

Journal of Ginseng Research
Van Binh NguyenTae-Jin Yang

Abstract

Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P.quinquefolius and P.trifolius) from North America and five (P.ginseng, P.notoginseng, P.japonicus, P.vietnamensis, and P.stipuleanatus) from Asia. We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in t...Continue Reading

Citations

Feb 4, 2021·Critical Reviews in Biotechnology·Nazish NehalRajinder K Gupta
Dec 29, 2020·Mitochondrial DNA. Part B, Resources·Guolun JiaPeng Li
Oct 26, 2018·Mitochondrial DNA. Part B, Resources·Seung Woo JinTae-Jin Yang
Aug 23, 2018·Mitochondrial DNA. Part B, Resources·Shin-Jae KangTae-Jin Yang
Feb 21, 2021·Genes & Genomics·Hyeonah ShimTae-Jin Yang
May 11, 2021·Mitochondrial DNA. Part B, Resources·Young Sang ParkTae-Jin Yang

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Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

MAFFT
Artemis
Circos
MEGA
dnaLCW

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