Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 704-706 |
| Number of pages | 3 |
| Journal | Mitochondrial DNA Part B: Resources |
| Volume | 2 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 2017 Dec 20 |
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Keywords
- endangered species
- Habenaria radiata
- Orchidaceae
- plastome
ASJC Scopus subject areas
- Genetics
- Molecular Biology
Cite this
The complete plastome sequence of the endangered orchid Habenaria radiata (Orchidaceae). / Kim, Young Kee; Kwak, Myoung Hai; Hong, Ja Ram; Kim, Hoe Won; Jo, Sangjin; Sohn, Jung Yeon; Cheon, Se Hwan; Kim, Ki-Joong.
In: Mitochondrial DNA Part B: Resources, Vol. 2, No. 2, 20.12.2017, p. 704-706.Research output: Contribution to journal › Article
}
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
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 - endangered species
KW - Habenaria radiata
KW - Orchidaceae
KW - plastome
UR - http://www.scopus.com/inward/record.url?scp=85031407848&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85031407848&partnerID=8YFLogxK
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 -