The complete plastome sequence of the endangered orchid Oberonia japonica (Orchidaceae)

Young Kee Kim, Myoung Hai Kwak, Myong Gi Chung, Hoe Won Kim, Sangjin Jo, Jung Yeon Sohn, Se Hwan Cheon, Ki-Joong Kim

Research output: Contribution to journalArticle

Abstract

In this study, we report the complete chloroplast sequence of Oberonia japonica (Maxim.) Makino (Orchidaceae) (NCBI acc. no. KX871235), which is an endangered plant species currently protected by the National Law of Korea. The gene order and content of the O. japonica plastome are similar to those of a typical orchid plastome. The 11 ndh genes are pseudogenized or lost completely from the plastome of O. japonica. The plastome contains 102 genes, of which 68 are protein-coding genes, 30 and four are transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, respectively. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. The complete plastome is 142,996 bp long and consists of one large and small single copy each of 81,669 and 10,969 bp, respectively, separated by two inverted repeats of 25,179 bp. The AT content of the O. japonica plastome is 62.6%. Sixty-five simple sequence repeat (SSR) loci, consisting of 56 mono-SSR, seven di-SSR, and two tri-SSR are scattered along the O. japonica plastome. Some of these plastome SSR loci may be useful for developing genetic markers for the O. japonica populations. Phylogenetic analysis has shown that O. japonica is a member of the Malaxideae. The genus Oberonia forms a monophyletic clade with Dendrobium.

Original languageEnglish
Pages (from-to)711-713
Number of pages3
JournalMitochondrial DNA Part B: Resources
Volume2
Issue number2
DOIs
Publication statusPublished - 2017 Dec 20

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Orchidaceae
Microsatellite Repeats
Introns
Genes
Dendrobium
Endangered Species
Gene Order
Chloroplasts
Korea
Genetic Markers
rRNA Genes
Population
Proteins

Keywords

  • endangered species
  • ndh gene family loss
  • Oberonia japonica
  • Orchidaceae
  • Platome

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

The complete plastome sequence of the endangered orchid Oberonia japonica (Orchidaceae). / Kim, Young Kee; Kwak, Myoung Hai; Chung, Myong Gi; 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. 711-713.

Research output: Contribution to journalArticle

Kim, Young Kee ; Kwak, Myoung Hai ; Chung, Myong Gi ; Kim, Hoe Won ; Jo, Sangjin ; Sohn, Jung Yeon ; Cheon, Se Hwan ; Kim, Ki-Joong. / The complete plastome sequence of the endangered orchid Oberonia japonica (Orchidaceae). In: Mitochondrial DNA Part B: Resources. 2017 ; Vol. 2, No. 2. pp. 711-713.
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