Abstract
Panax japonicus var. major (Araliaceae) is an important medicinal plant, whose rhizomes have pharmacological activities such as protection of cardiovascular and cerebrovascular system, central nervous system and so on. In this study, we sequenced complete chloroplast (cp) genome sequence of P. japonicus var. major so as to explore phylogenetic relationship between this species and related species. The results showed that complete cp genome of P. japonicus var. major was 156,402 bp in length, consisting of a large single copy (LSC) region of 86,187 bp, a small single copy (SSC) region of 18,007 bp, and two inverted repeat regions (IRa and IRb) of 26,104 bp. In total, 114 genes were annotated, comprising of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that P. japonicus var. major was closely related to its original variety, P. japonicus var. japonicus; meanwhile, Panax was a monophyletic group with high support value and it had a close relationship with Aralia in Araliaceae.