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

doi:10.1080/23802359.2017.1390409

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 journal › Article › peer-review

2 Citations (Scopus)

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 language	English
Pages (from-to)	711-713
Number of pages	3
Journal	Mitochondrial DNA Part B: Resources
Volume	2
Issue number	2
DOIs	https://doi.org/10.1080/23802359.2017.1390409
Publication status	Published - 2017 Dec 20

Bibliographical note

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.

Publisher Copyright:
© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

Keywords

Oberonia japonica
Orchidaceae
Platome
endangered species
ndh gene family loss

ASJC Scopus subject areas

Molecular Biology
Genetics

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10.1080/23802359.2017.1390409

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title = "The complete plastome sequence of the endangered orchid Oberonia japonica (Orchidaceae)",

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.",

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author = "Kim, {Young Kee} and Kwak, {Myoung Hai} and Chung, {Myong Gi} and Kim, {Hoe Won} and Sangjin Jo and Sohn, {Jung Yeon} and Cheon, {Se Hwan} and Kim, {Ki Joong}",

note = "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. Publisher Copyright: {\textcopyright} 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.",

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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