title: The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion.
abstract: Endemic to the Sino-Himalayan subregion, the medicinal alpine plant Gentiana straminea is a threatened species. The genetic and molecular data about it is deficient. Here we report the complete chloroplast (cp) genome sequence of G. straminea, as the first sequenced member of the family Gentianaceae. The cp genome is 148,991bp in length, including a large single copy (LSC) region of 81,240bp, a small single copy (SSC) region of 17,085bp and a pair of inverted repeats (IRs) of 25,333bp. It contains 112 unique genes, including 78 protein-coding genes, 30 tRNAs and 4 rRNAs. The rps16 gene lacks exon2 between trnK-UUU and trnQ-UUG, which is the first rps16 pseudogene found in the nonparasitic plants of Asterids clade. Sequence analysis revealed the presence of 13 forward repeats, 13 palindrome repeats and 39 simple sequence repeats (SSRs). An entire cp genome comparison study of G. straminea and four other species in Gentianales was carried out. Phylogenetic analyses using maximum likelihood (ML) and maximum parsimony (MP) were performed based on 69 protein-coding genes from 36 species of Asterids. The results strongly supported the position of Gentianaceae as one member of the order Gentianales. The complete chloroplast genome sequence will provide intragenic information for its conservation and contribute to research on the genetic and phylogenetic analyses of Gentianales and Asterids.
authors.affiliation: School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, China.
authors.forename: Lianghong
authors.initials: L
authors.lastname: Ni
authors.affiliation: School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, China. Electronic address: zhilzhao@163.com.
authors.forename: Zhili
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, China.
authors.forename: Hongxi
authors.initials: H
authors.lastname: Xu
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 16 Nanxiao street, Beijing, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Chen
authors.affiliation: Tibetan Traditional Medical College, 10 Dangre Middle Road, Lhasa, China.
authors.forename: Gaawe
authors.initials: G
authors.lastname: Dorje
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D054628:Genome, Chloroplast; D030012:Gentiana / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D018749:RNA, Plant / Q000235:genetics
chemical_list: D018749:RNA, Plant
keywords: Asterids; Chloroplast genome; Gentiana straminea; Gentianaceae; Phylogenetics; Sino-Himalayan subregion