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The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum (Cnidaria: Anthozoa) using next-generation sequencing

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  • Chengde Medical University, Chengde, Hebei Province, China;

Abstract

The complete mitochondrial genome of Sarcophyton trocheliophorum was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,508 bp in length, containing 14 protein-coding genes, two ribosomal RNA genes and one transfer RNA gene (Met-tRNA). The base composition is 30.45% A, 16.03% C, 19.13% G, and 34.40% T, with an A + T content of 64.85%. A phylogenetic analysis of Alcyoniidae showed that genus Sarcophyton had the closest relationship with Sinularia.
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The complete mitochondrial genome of soft coral
Sarcophyton trocheliophorum (Cnidaria: Anthozoa)
using next-generation sequencing
Chun-Yang Shen, Ya-Ting Dan, Alireza Asem, Pei-Zheng Wang, Wei Xue, Xiao-
Bo Tong & Weidong Li
To cite this article: Chun-Yang Shen, Ya-Ting Dan, Alireza Asem, Pei-Zheng Wang, Wei Xue,
Xiao-Bo Tong & Weidong Li (2019) The complete mitochondrial genome of soft coral Sarcophyton
trocheliophorum (Cnidaria: Anthozoa) using next-generation sequencing, Mitochondrial DNA Part
B, 4:2, 3734-3735, DOI: 10.1080/23802359.2019.1679677
To link to this article: https://doi.org/10.1080/23802359.2019.1679677
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 24 Oct 2019.
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MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of soft coral Sarcophyton trocheliophorum
(Cnidaria: Anthozoa) using next-generation sequencing
Chun-Yang Shen
a
, Ya-Ting Dan
b
, Alireza Asem
b
, Pei-Zheng Wang
b
, Wei Xue
c
, Xiao-Bo Tong
d
and
Weidong Li
b
a
Department of Biology, Chengde Medical University, Chengde, Hebei Province, China;
b
College of Fisheries and Life Science, Hainan
Tropical Ocean University, Sanya, China;
c
Department of Chemical Engineering, Chengde Petroleum College, Chengde, China;
d
Department
of Physiology, Chengde Medical University, Chengde, Hebei Province, China
ABSTRACT
The complete mitochondrial genome of Sarcophyton trocheliophorum was completed using next-
generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,508 bp in
length, containing 14 protein-coding genes, two ribosomal RNA genes and one transfer RNA gene
(Met-tRNA). The base composition is 30.45% A, 16.03% C, 19.13% G, and 34.40% T, with an A þTcon-
tent of 64.85%. A phylogenetic analysis of Alcyoniidae showed that genus Sarcophyton had the closest
relationship with Sinularia.
ARTICLE HISTORY
Received 10 July 2019
Accepted 25 September 2019
KEYWORDS
Mitogenome; soft coral;
Sarcophyton
trocheliophorum; base
composition; phylogenetic
analysis
Species of soft coral genus Sarcophyton are widespread, from
Polynesia in the east to the Red Sea in the west. Usually,
they habitat in marine environment from the intertidal zone
to depths up to 15 m. Colonies of Sarcophyton are character-
istically fleshy and soft, mainly mushroom shape with yellow,
beige, brown or green colour (Feussner and Waqa 2013).
Incomplete mitogenome of Sarcophyton glaucum is the
only sequence in genus Sarcophyton, contains 11,715 bp
(Beaton et al. 1998). In this study, we submitted and analyzed
the first complete mitogenome of Sarcophyton,Sarcophyton
trocheliophorum (GenBank: MK994517).
An individual of S. trocheliophorum was collected from the
South China Sea (West Island, Sanya, Hainan province, China;
181408.7500N, 10922039.1000 E) and stored in Hainan Tropical
Ocean University Museum of Zoology (NO.0001-St). The spe-
cimen was identified using mtMutS haplotype similarity. A
genomic library was established followed by paired-end
(2 150 bp) next-generation sequencing (10 Gb), using the
Illumina HiSeq X-ten sequencing platform. The quality of pro-
duced sequencing reads was checked by FastQC (Andrews
2010). The sequences were assembled and mapped to the
reference Sinularia mitochondrial genome (Sinularia peculiaris,
JX023274) with Spades v3.9.0 (Bankevich et al. 2012) and
bowtie v2.2.9 (Langmead and Salzberg 2012). Protein-coding
genes (PCGs) and ribosomal RNA genes (rRNAs) were identi-
fied by alignment to the Sinularia peculiaris mitochondrial
genome (GenBank: JX023274) and using online server NCBI
ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html).
The determination of the putative transfer RNA gene
(tRNAs) was performed by online software ARWEN (http://
130.235.46.10/ARWEN/) and tRNAscan-SE2.0 (http://lowelab.
ucsc.edu/tRNAscan-SE/).
The complete mitogenome of S. trocheliophorum was
18,508 in length, with a nucleotide composition of 30.45% A,
16.03% C, 19.13% G and 34.40% T.
The structure of S. trocheliophorum mitogenome was sig-
nificantly different from classic metazoan mitogenomes,
which contain 13 PCGs, 2 rRNAs and 22tRNAs.
The gene content and gene order in present mitoge-
nome are the same as in the other Alcyoniidae, which
include 14 PCGs, 2 rRNAs and 1 tRNA. Twelve genes (cox1,
12S, nad1, cytb, nad6, nad3, nad4L, mutS, 16S, nad2, nad5,
and nad4) were located on the heavy strand and the other
five genes (tRNA-Met, cox3, atp6, atp8 and cox2) were
encoded on the light strand. All PCGs were detected to
start with the ATG codon. Seven genes (nad1, nad6, nad3,
nad2, nad5, cox3 and cox2) appeared to use TAG as stop
codon, whereas six genes (cytb, nad4L, mutS, nad4, atp6,
and atp8) use the stop codon TAA, and cox1 use no pre-
mature stop codon T. We found that there was only one
tRNA (Met-tRNA) that can be folded into typical clover-leaf
secondary structures. There were a total of 15 gaps
between coding genes, the length of which ranged from 3
nucleotides to 112 nucleotides. A 13 nucleotide overlap
existed between nad2 and nad5, which was the same as
Sinularia peculiaris. The whole mitogenome possessed
CONTACT Chun-Yang Shen scyshenchunyang@yeah.net Department of Biology, Chengde Medical University, Chengde 067000, Hebei Province, China;
Weidong Li 542148880@qq.com College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya 572000, China
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, 37343735
https://doi.org/10.1080/23802359.2019.1679677
strong A þT content bias. A þT content of the overall
mitogenome was 64.85%, and A þT content of PCGs,
rRNAs, and tRNA was 66.26, 58.7, and 56.34%, respectively.
A phylogenetic analysis of family Alcyoniidae was estab-
lished based on 7 known Alcyoniidae mitogenomes (Beaton
et al. 1998; Brockman and Mcfadden 2012; Kayal et al. 2013;
Figueroa and Baco 2015; Shimpi et al. 2017; Asem et al.
2019) and an outgroup (Chrysopathes Formosa) (Brugler and
France 2007). The concatenated dataset for nucleotides con-
tained nine PCGs (published S. glaucum mitogenome lacks
nad3, nad4L, nad6, cytb, and mutS) (Beaton et al. 1998). The
maximum-likelihood (ML) phylogenetic analysis was per-
formed based on the concatenated dataset by using the soft-
ware MEGA X (Kumar et al. 2018). Regarding to phylogenetic
tree, genera Sarcophyton and Sinularia revealed close evolu-
tionary relationship (Figure 1).
Disclosure statement
The authors report no conflicts of interest. The authors alone are respon-
sible for the content and writing of the manuscript.
Funding
This project was funded by Science and Technology Research Project of
Higher Education in Hebei Province [QN2019093], Research Project of
Chengde Medical University [201601] and Hainan Province Science and
Technology Department Key Research and Development Programme
[ZDYF2019154].
ORCID
Alireza Asem http://orcid.org/0000-0002-8991-4903
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Figure 1. Phylogenetic tree of Alcyoniidae based on the concatenated nucleotides of nine protein coding genes and two rRNA genes using maximum-likelihood
(ML). Numbers behind each node denote the bootstrap support values.
MITOCHONDRIAL DNA PART B 3735
... The new present mitogenome and all sequences mitogenomes in Alcyoniidae were used in phylogenetic analysis (Brockman and Mcfadden 2012;Kayal et al. 2013;Figueroa and Baco 2015;Shimpi et al. 2017;Asem et al. 2019;Chen et al. 2019;Shen et al. 2019), and Briareum asbestinum (Medina et al. 2006) was set for the outgroup. The concatenated dataset for nucleotides including all 14 PCGS and two rRNAs were performed to draw phylogenetic tree using the maximum-likelihood method (ML). ...
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