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The complete chloroplast genome sequence of Goodyera schlechtendaliana in Korea (Orchidaceae)

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Goodyera schlechtendaliana is a common orchid species in East Asia, providing a case to study phylogeographic structure of understory plants in warm temperate forests. Here, we present the complete chloroplast genome of the Korean G. schlechtendaliana. Its length is 153,801 bp and it has four subregions; 82,683 bp of large-single-copy and 18,048 bp of small-single-copy regions are separated by 26,535 bp of inverted repeat regions, including 133 genes (86 protein-coding genes, eight rRNAs, and 39 tRNAs). Phylogenetic analyses suggest that the chloroplast genomic data should be useful in future phylogeographic and phylogenetic studies of Goodyera.
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The complete chloroplast genome sequence of
Goodyera schlechtendaliana in Korea (Orchidaceae)
Sang-Hun Oh, Hwa Jung Suh, Jongsun Park, Yongsung Kim & Sangtae Kim
To cite this article: Sang-Hun Oh, Hwa Jung Suh, Jongsun Park, Yongsung Kim & Sangtae Kim
(2019) The complete chloroplast genome sequence of Goodyera�schlechtendaliana in Korea
(Orchidaceae), Mitochondrial DNA Part B, 4:2, 2692-2693, DOI: 10.1080/23802359.2019.1641439
To link to this article: https://doi.org/10.1080/23802359.2019.1641439
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 24 Jul 2019.
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MITOGENOME ANNOUNCEMENTS
The complete chloroplast genome sequence of Goodyera schlechtendaliana in
Korea (Orchidaceae)
Sang-Hun Oh
a
, Hwa Jung Suh
b
, Jongsun Park
c,d
, Yongsung Kim
c,d
and Sangtae Kim
b
a
Department of Biology, Daejeon University, Daejeon, Korea;
b
Department of Biology, Sungshin University, Seoul, Korea;
c
Infoboss Co., Ltd.,
Seoul, Korea;
d
InfoBoss Research Center, Seoul, Korea
ABSTRACT
Goodyera schlechtendaliana is a common orchid species in East Asia, providing a case to study phylo-
geographic structure of understory plants in warm temperate forests. Here, we present the complete
chloroplast genome of the Korean G. schlechtendaliana. Its length is 153,801bp and it has four subre-
gions; 82,683 bp of large-single-copy and 18,048 bp of small-single-copy regions are separated by
26,535 bp of inverted repeat regions, including 133 genes (86 protein-coding genes, eight rRNAs, and
39 tRNAs). Phylogenetic analyses suggest that the chloroplast genomic data should be useful in future
phylogeographic and phylogenetic studies of Goodyera.
ARTICLE HISTORY
Received 17 June 2019
Accepted 22 June 2019
KEYWORDS
Goodyera; chloroplast
genome; Goodyera
schlechtendaliana; Korea;
Orchidaceae
Goodyera schlechtendaliana Rchb. f. (Orchidaceae) is a com-
mon orchid widely distributed in the Himalayas, Sumatra,
China, Taiwan, Korea, and Japan, occupying shady places
with moist and well-drained soils. It is characterized by hav-
ing creeping rhizomes, white variegated markings on the
adaxial surfaces of the leaves, saccate labellum, two sectile
pollinia attached to a viscidium, and a single stigmatic lobe
in Orchidaceae (Chen et al. 2009; Hu et al. 2016). It is often
cultivated as an ornamental because of the patterns on the
leaves. Both sexual and clonal reproduction occur in G.
schlechtendaliana (Brzosko et al. 2013). Phylogeographic
structure representing differentiation among populations has
not been studied despite the wide distribution range of the
species. Chloroplast genome is useful to trace the seed
movement and infer the geographic structure.
The complete chloroplast genome of G.schlechtendaliana
from southern part of Korea (3441023.2800N, 12511048.4900 E)
was determined to be used in understanding of infraspecific
variation. Total DNA was extracted from fresh leaves collected
on Hongdo Island in Shinan-gun, Jeollanam-do, Korea (vou-
cher in the herbarium of Daejeon University (TUT); Oh 7171)
using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany).
Paired-end sequencing was performed using HiSeq4000
(Illumina, San Diego, USA) of Macrogen Inc., Korea. De novo
assembly was performed using Velvet 1.2.10 (Zerbino and
Birney 2008), and gap sequences were filled by
SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013),
and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5
(Biomatters Ltd., Auckland, New Zealand) was used for gen-
ome annotation based on G. schlechtendaliana chloroplast
genome (MK134679; Oh et al. 2019).
The chloroplast genome of Korean G. schlechtendaliana
(GenBank accession: MK144665) is 153,801 bp (the GC-ratio is
37.2%) and has four subregions: 82,683 bp of large-single-
copy (GC-ratio, 34.9%) and 18,048 bp of small-single-copy
(GC-ratio, 29.7%) regions are separated by 26,535 bp each of
inverted repeats (IR; GC-ratio, 43.3%). It contains 133 genes
(86 protein-coding genes, eight rRNAs, and 39 tRNAs) with
19 genes (seven protein-coding genes, four rRNAs, and eight
tRNAs) duplicated in the IR regions.
Twelve complete chloroplast genomes, includig eight from
four species of Goodyera, two from closely allied groups, and
two outgroups, were aligned using MAFFT 7.388 (Katoh and
Standley 2013). Phylogenetic trees were constructed using
the neighbor-joining (with 10,000 bootstrap repeats) and
maximum likelihood methods (with 1000 bootstrap repeats)
in MEGA X (Kumar et al. 2018).
The phylogenetic tree shows that G. schlechtendaliana
from Korea forms strongly supported clade with other acces-
sions of G.schlechtendaliana from China (Figure 1A). The
result agrees with morphology and previous phylogenetic
analysis based on nuclear ITS regions (Hu et al. 2016).
Comparison of five chloroplast genomes of G.schlechtendali-
ana showed 200844 single nucleotide polymorphisms and
4142133 insertions and deletions among accessions (Figure
1B), suggesting a high level of infraspecific variation com-
pared with those in Pseudostellaria (Kim et al. 2019) and
Coffea (Park et al. 2019). The chloroplast genome will be a
useful resource for investigation of phylogeographic structure
within G.schlechtendaliana and for understanding phylogen-
etic relationship of Goodyera.
CONTACT Sang-Hun Oh soh42@dju.kr Department of Biology, Daejeon University, Daejeon 34520, Korea; Sangtae Kim amborella@sungshin.ac.kr
Department of Biology, Sungshin University, Seoul 01133, Korea
ß2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
MITOCHONDRIAL DNA PART B
2019, VOL. 4, NO. 2, 26922693
https://doi.org/10.1080/23802359.2019.1641439
Disclosure statement
No potential conflict of interest was reported by the authors.
Funding
This work was supported by a research grant from the National Research
Foundation of Korea [NRF-2016R1D1A1B03934663] to the first author.
ORCID
Sang-Hun Oh http://orcid.org/0000-0001-8778-4458
Jongsun Park http://orcid.org/0000-0003-0786-4701
Yongsung Kim http://orcid.org/0000-0002-5349-9226
Sangtae Kim http://orcid.org/0000-0002-1821-4707
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MK134679 Goodyera schlechtendaliana
MK144665 Goodyera schlechtendaliana
NC_029364 Goodyera schlechtendaliana
KJ501999 Goodyera fumata
KT886429 Goodyera procera
KT886432 Goodyera veluna
NC_030540 Ludisia discolor
NC_030722 Apostasia odorata
100/100
100/100
100/100
100/100
99/82
100/100
100/100
100/100
99/100
AB893949 Goodyera schlechtendaliana
LC085346 Goodyera schlechtendaliana
NC_033895 Anoectochilus emeiensis
NC_026778 Vanilla planifolia
0.05 substuons/site
NC_029364
AB893949
LC085346
200/ 511
700/ 1,066
844/ 2,045
282/ 1,060
827/ 1,794
163/651
740/ 1,470
597/ 1,065 445/ 414
700/ 2,133
# of SNPs/# of INDELs
MK144665
MK134679
(A) (B)
Figure 1. (A) A maximum-likelihood tree using chloroplast genomes of G. schlechtendaliana from Korea (MK144665 in this study and MK134679) and previously
published related taxa: G. schlechtendaliana from China (AB892949, LC085346, and NC_029364), G. fumata (KJ501999), G. procera (KT886429), G. velutina
(KT886432), Ludisia discolour (NC_030540), Anoectochilus emeiensis (NC_033895), and two outgroup species, Vanila planifolia (NC_026778) and Apostasia odorata
(NC_030722). Bootstrap values using the neighbor-joining and maximum-likelihood methods are indicated above the branch. (B) Pairwise comparisons of five
chloroplast genomes of G. schlechtendaliana. Numbers of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) between each pair are indi-
cate on the branch. Filled eclipses indicate G. schlechtendaliana originated from Korea and opened eclipses mean G. schlechtendaliana originated from China.
MITOCHONDRIAL DNA PART B 2693
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