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MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of soft coral, Eleutherobia rubra (Brundin,
1896) (Cnidaria; Anthozoa; Malacalcyonacea; Alcyoniidae)
Chi-Hyeon Kim
a
, Sang-Hwa Lee
b
, In-Young Cho
a
, Min-Seop Kim
a
, Seonock Woo
c
,
Keun-Yong Kim
d
and Sung-Jin Hwang
e
a
National Marine Biodiversity Institute of Korea, Seocheon, South Korea;
b
Invertebrate Diversity Institute (InDI), Cheongju, South Korea;
c
Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea;
d
AquaGenTech Co., Ltd.,
Busan, South Korea;
e
Department of Life Science, Woosuk University, Jincheon, South Korea
ABSTRACT
The mitogenome of a soft coral, Eleutherobia rubra (Brundin, 1896), was completely sequenced for the
first time. The total mitogenome length of E. rubra is 18,724 bp with 14 protein-coding genes, two ribo-
somal RNA genes, one transfer RNA gene (tRNA–Met), and one non-coding region (NCR). The gene
order is also consistent with other Alcyoniidae species. The base composition is 30.1% A, 16.7% C,
19.5% G, and 33.7% T, with a G–C content of 36.2%. This is the first record of the complete mitoge-
nome sequence of the genus Eleutherobia.
ARTICLE HISTORY
Received 25 May 2023
Accepted 20 September 2023
KEYWORDS
Eleutherobia rubra; soft
coral; Alcyoniidae; complete
mitogenome; phylogenetic
analysis
Introduction
Eleutherobia rubra (Brundin, 1896) belonging to Alcyoniidae is
a finger-shaped azooxanthellate soft coral. Since Eleutherobia
was first reported by P€
utter in 1900, 13 species are known to
date. Eleutherobia rubra inhabits the temperate waters
around Korea, Japan, the USA (California), and Australia, at
depths of 20–182 m (Song 1976; Verseveldt and Bayer 1988;
Imahara et al. 2014). In Korea, this species occurs in a wide
area around the western, southern, and eastern coasts, and
forms several populations with high density, particularly in
the coastal sea off the south coast of Korea (Figure 1).
However, these populations are threatened by global warm-
ing. The Kuroshio, which transports excess heat from tropical
ocean to the north in the western North Pacific, has warmed
twice to three times faster than the global average (Wang
et al. 2016; Lam et al. 2021; Sasaki and Umeda 2021; Wan
et al. 2023). Consequently, the East Asian marginal seas
including Korean peninsula, which are strongly affected by
the Kuroshio Current, have become rapidly warming regions
(Wang and Wu 2022; Lee et al. 2023). Recently, loss of these
populations and changes in transcription and symbiotic bac-
terial composition have been observed due to thermal stress
(Lee et al. 2020, 2023). Coral bleaching and mass mortality
due to heatwaves have also been observed worldwide,
including in the Mediterranean and the Great Barrier Reefs
(Hughes et al. 2017; Garrabou et al. 2022; McGowan and
Theobald 2023).
Populations with rapidly decreasing population sizes are
easily at risk of extinction due to loss of genetic diversity
(Kliman et al. 2008). Genetic management of species at risk
of potentially endangered and resolving taxonomic uncer-
tainties using genetic markers are important factors in con-
servation genetics (Frankham 2019; Hoban et al. 2023).
Therefore, as the beginning of efforts to conserve the E. rubra
population by identifying and managing genetic diversity
using mitochondrial markers, the E. rubra mitogenome was
analyzed. Approximately, 3,290 species of octocorals are
known worldwide, but mitogenome data have been reported
from only 6.7% (about 221 species) species so far (NCBI 2023;
WoRMS Editorial Board 2023). This is the first report of the
complete mitogenome in Eleutherobia. In addition, these data
will also provide valuable information for further studies on
the molecular taxonomy and phylogeny of octocorals, which
are problematic in their taxonomy due to limited range of
morphological characters, and insufficient and inadequate
descriptions (Kessel et al. 2023).
Materials and methods
One specimen of E. rubra was collected from the subtidal zone
of Eoyu Island in the coastal sea off the south coast of Korea
(34�39034.5800 N, 128�34031.4300 E), and deposited at the
Cnidaria Bioresources Bank of Korea, Woosuk University,
Jincheon, South Korea (voucher number: CBB17CnAnE226, Prof.
Sung-Jin Hwang, buteo2@woosuk.ac.kr). For identification,
CONTACT Sung-Jin Hwang buteo2@woosuk.ac.kr, buteo2@gmail.com Department of Life Science, Woosuk University, Jincheon, South Korea
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2023.2263198.
� 2023 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-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits
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MITOCHONDRIAL DNA PART B: RESOURCES
2023, VOL. 8, NO. 10, 1059–1062
https://doi.org/10.1080/23802359.2023.2263198
detailed morphological characteristics of the sclerites were con-
firmed following Song (1976).
Total genomic DNA was extracted from the polyp tissue
of the voucher specimen using the phenol–chloroform
method using a lysis buffer containing high concentration of
urea (10mM Tris–HCl, pH 8.0; 125 mM NaCl; 10 mM EDTA, pH
8.0; 1% SDS; 8 M urea) developed by Asahida et al. (1996).
The complete mitogenome sequence was amplified using
long-range PCR (LR-PCR), and then three LR-PCR products
covering whole mitochondrial genome were sequenced by
the primer walking method with 26 primers newly designed
in this study (Table S1 for primers and Figure S1 for PCR gel
image). The PCR reaction solutions were made using
AccuPower ProFi Taq PCR PreMix (Bioneer, Daejeon, South
Korea), and PCR amplification was performed according to
the user manual of the ProFlex PCR System (Life
Technologies, Carlsbad, CA). LR-PCR products were directly
sequenced using 3730xl DNA Analyzer (Applied Biosystems,
Foster City, CA).
The complete circular mitogenome sequence of E. rubra
was assembled starting with COX1 partial sequences as the
first location in the gene map, the circular form was deter-
mined by identifying overlapped sequences between the first
and the last partial sequences and compared the completed
sequence with other mitogenome sequences in Alcyoniidae
species. All LR-PCR sequences were checked and corrected
during the assembly process using Geneious 9.1.8
(Biomatters, Auckland, New Zealand) (Kearse et al. 2012). The
14 protein-coding genes (PCGs) were annotated by identify-
ing their open reading frames (ORFs), and by comparing
them with other reported mitogenomes of Alcyoniidae spe-
cies using MITOS web server (Bernt et al. 2013). The two ribo-
somal RNA genes (rRNAs) and one transfer RNA gene were
determined by comparison with homologous gene sequences
of other Alcyoniidae mitochondrial genomes.
The phylogenetic analysis was performed using mitoge-
nomes sequences of eight previously published Alcyoniidae
(Muthye et al. 2022) and the E. rubra in this study. Two
Xeniidae mitogenomes were used as outgroup. Mitogenome
sequences (14 PCGs nucleotides, excluding stop codons) of a
total 11 species including E. rubra were concatenated and
aligned using the multiple sequence alignment program,
MAFFT v.7 (Katoh and Standley 2013) for phylogenetic ana-
lysis. A phylogenetic tree was reconstructed based on the
concatenated dataset using the maximum-likelihood (ML)
method with the GTR þG þI model in raxmlGUI 2.0 (Edler
et al. 2021), with the bootstrap values being calculated from
10,000 replicates.
Results
The complete circular mitogenome of E. rubra was 18,724 bp
in length (GenBank accession no. ON814482) (Figure 2),
which was within published mitogenome lengths for
Alcyoniids (18–19 kb). MutS gene, which is involved in DNA
repair in octocoral mitochondria, was found in E. rubra mito-
genome. Recently, the gene was utilized as a highly effective
molecular marker for phylogenetic analysis in the octocoral
Figure 1. Eleutherobia rubra. (A) Population in the coastal sea off the south coast of Korea. (B) Voucher specimen used in this study. Photographs of habitat and
voucher were taken by Seung-Hwan Park (underwater photographer at H Dive) and Chi-Hyeon Kim, respectively, and copyright license agreements were obtained.
Figure 2. Circular representation of the complete mitogenome for E. rubra. The
genes were colored based on their functional groups. Arrows show the direc-
tions of transcription.
1060 C.-H. KIM ET AL.
group (McFadden et al. 2022; Muthye et al. 2022). E. rubra
mitogenome has 17 genes (14 PCGs, two rRNAs, and one
transfer RNA gene (tRNA–Met)) and one non-coding region
(NCR) of 109 bp. The gene order shows an ancestral octocoral
mt gene order, consistent with other Alcyoniidae species
(Figueroa and Baco 2015). Regarding its nucleotide base
composition, this mitogenome has A, C, G, and T contents of
30.1%, 16.7%, 19.5%, and 33.7%, respectively, with a G þC
content of 36.2%. Two rRNAs (rrnS and rrnL) and 10 PCGs
were encoded by the heavy strand. Four PCGs (ATP6, ATP8,
COX2, and COX3) and tRNA–Met were encoded by the light
strand. All PCGs began with ATG as a start codon. In addition,
all PCGs used TAR as a stop codon. Ten genes (ATP8, COX1–3,
COB, ND1–3, ND5, and ND6) ending with TAG and four genes
(ATP6, MutS, ND4, and ND4L) ended with TAA. The two rRNA
genes contained rrnS and rrnL between COX1 and ND1 or
between MutS and ND2. NCR was located between COX1 and
COX2.
Phylogeny analysis indicated that this new mitogenome
sequence of genus Eleutherobia clustered with Alcyonium spe-
cies in family Alcyoniidae (Figure 3). The tree showed that E.
rubra and A. acaule had a close relationship with a very high
nodal support (100% BP in ML). E. rubra and A. acaule shared
sequence similarities of 98% for the total length of mitoge-
nome sequences (18,724 bp of A. acaule). According to a pre-
vious study (McFadden et al. 2022), Eleutherobia species and
A. acaule belonged to a sister group in phylogenetic analysis
using MutS gene, similar to results of this study.
Discussion and conclusions
Through this study, we report the first complete mitogenome
sequencing with E. rubra for the genus Eleutherobia. The
results of this study can be used for the population conserva-
tion of E. rubra by identifying and managing genetic diversity
using mitochondrial genetic markers, and for comprehensive
taxonomic studies of the Alcyoniidae including this species
as a representative of the genus Eleutherobia.
Author contributions
Chi-Hyeon Kim: data analysis and manuscript writing. Sang-Hwa Lee:
mapping and phylogenetic analysis. In-Young Cho: identification and
manuscript revising. Min-Seop Kim: manuscript reviewing. Seonock Woo:
manuscript reviewing. Keun-Yong Kim: data collection and analysis.
Sung-Jin Hwang: designing this study, manuscript reviewing, and
approval of final version to be published.
Ethical approval
This research does not involve ethical research. However, the sample col-
lection area was designated and protected as Hallyeohaesang National
Park, so the sample was collected with permission from the Korea
National Park Service. E. rubra is widespread in South Korea, and is not
listed as a threatened or endangered species.
Disclosure statement
The authors declare no conflict of interest. The authors alone are respon-
sible for the content and writing of the paper.
Funding
This work was supported by a grant from the National Marine
Biodiversity Institute of Korea under Grant [2023M00300].
Figure 3. Maximum-likelihood tree based on concatenated 14 PCGs sequence dataset from 11 Malacalcyonacea species. Two Xeniidae species (Anthelia glauca and
Caementabunda simplex) were used as outgroups. GenBank accession numbers of each sequence are marked behind their corresponding species names in the tree.
Sequence obtained in this study is in bold.
MITOCHONDRIAL DNA PART B: RESOURCES 1061
ORCID
Chi-Hyeon Kim http://orcid.org/0000-0002-7086-3878
Sang-Hwa Lee http://orcid.org/0000-0002-1828-705X
In-Young Cho http://orcid.org/0000-0002-0979-7971
Min-Seop Kim http://orcid.org/0000-0003-2735-5103
Seonock Woo http://orcid.org/0000-0001-6491-1450
Keun-Yong Kim http://orcid.org/0000-0002-7647-3766
Sung-Jin Hwang http://orcid.org/0000-0002-1259-6775
Data availability statement
The data that support the findings of this study are openly available in
the GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the acces-
sion ON814482. The associated BioProject, SRA and Bio-sample numbers
are PRJNA930047, SRR24682002, and SAMN29133432, respectively.
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