TY - JOUR
T1 - The complete plastome sequence of the endangered orchid Habenaria radiata (Orchidaceae)
AU - Kim, Young Kee
AU - Kwak, Myoung Hai
AU - Hong, Ja Ram
AU - Kim, Hoe Won
AU - Jo, Sangjin
AU - Sohn, Jung Yeon
AU - Cheon, Se Hwan
AU - Kim, Ki Joong
N1 - Funding Information:
This work was supported by a genome research grant for endangered species in Korea from the National Institute of Biological Resources [NIBR 201603203]. Addition funds also provided by the National Research Foundation of Korea [NRF-2015M3A9B8030588 and NRF-2015M3A9B8047398] to KJK.
PY - 2017/12/20
Y1 - 2017/12/20
N2 - In this study, we determined the complete chloroplast sequence of Habenaria radiata (Thunb.) Spreng. (Orchidaceae) (NCBI acc. no. KX871237), an endangered plant species protected by the national law of Korea. The gene order and gene content of the H. radiata plastome are similar to those of typical angiosperm plastomes. The 11 ndh genes, which are usually lost in orchid plastomes, are intact in the H. radiata plastome. The complete plastome is 155,353 bp in length and consists of a large single copy of 84,833 bp and a small single copy of 17,718 bp, separated by two inverted repeats of 26,401 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes (clpP, ycf3) have two introns. A total of 76 simple sequence repeat (SSR) loci, which consist of 58 mono-SSR, 17 di-SSR, and 1 tri-SSR, are scattered along the H. radiata plastome. Some of these plastome SSR and high sequence divergent regions may be useful for development of genetic markers for the populations of H. radiata and other congeneric species. Phylogenetic analysis identified the sister relationship between H. radiata and H. pantlingiana within the tribe Orchideae.
AB - In this study, we determined the complete chloroplast sequence of Habenaria radiata (Thunb.) Spreng. (Orchidaceae) (NCBI acc. no. KX871237), an endangered plant species protected by the national law of Korea. The gene order and gene content of the H. radiata plastome are similar to those of typical angiosperm plastomes. The 11 ndh genes, which are usually lost in orchid plastomes, are intact in the H. radiata plastome. The complete plastome is 155,353 bp in length and consists of a large single copy of 84,833 bp and a small single copy of 17,718 bp, separated by two inverted repeats of 26,401 bp. The plastome contains 113 genes, of which 79 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes (clpP, ycf3) have two introns. A total of 76 simple sequence repeat (SSR) loci, which consist of 58 mono-SSR, 17 di-SSR, and 1 tri-SSR, are scattered along the H. radiata plastome. Some of these plastome SSR and high sequence divergent regions may be useful for development of genetic markers for the populations of H. radiata and other congeneric species. Phylogenetic analysis identified the sister relationship between H. radiata and H. pantlingiana within the tribe Orchideae.
KW - Habenaria radiata
KW - Orchidaceae
KW - endangered species
KW - plastome
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U2 - 10.1080/23802359.2017.1390410
DO - 10.1080/23802359.2017.1390410
M3 - Article
AN - SCOPUS:85031407848
VL - 2
SP - 704
EP - 706
JO - Mitochondrial DNA Part B: Resources
JF - Mitochondrial DNA Part B: Resources
SN - 2380-2359
IS - 2
ER -