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The complete mitochondrial genome of Sinularia ceramensis Verseveldt, 1977 (Octocorallia: Alcyonacea) using next-generation sequencing

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Abstract

The complete mitochondrial genome of Sinularia ceramensis was completed using next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,740 bp in length. The gene arrangements including 14 protein-coding genes (PCGs), 2 rRNAs, and 1 tRNA (tRNA-Met). The base composition is 30.26% A, 16.44% C, 16.35% G, and 33.95% T, with a G + C content of 35.76%. According to the phylogenetic analysis, Alcyonacea family are clustered in different clades. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
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The complete mitochondrial genome of Sinularia
ceramensis Verseveldt, 1977 (Octocorallia:
Alcyonacea) using next-generation sequencing
Alireza Asem, Hao Lu, Pei-Zheng Wang & Weidong Li
To cite this article: Alireza Asem, Hao Lu, Pei-Zheng Wang & Weidong Li (2019) The
complete mitochondrial genome of Sinularia�ceramensis Verseveldt, 1977 (Octocorallia:
Alcyonacea) using next-generation sequencing, Mitochondrial DNA Part B, 4:1, 815-816, DOI:
10.1080/23802359.2019.1574678
To link to this article: https://doi.org/10.1080/23802359.2019.1574678
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Group.
Published online: 09 Feb 2019.
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MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Sinularia ceramensis Verseveldt, 1977
(Octocorallia: Alcyonacea) using next-generation sequencing
Alireza Asem
a
, Hao Lu
b
, Pei-Zheng Wang
a
and Weidong Li
a
a
College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China;
b
College of Ocean, Hainan University, Haikou, China
ABSTRACT
The complete mitochondrial genome of Sinularia ceramensis was completed using next-generation
sequencing (NGS) method. The mitochondrial genome is a circular molecule of 18,740 bp in length.
The gene arrangements including 14 protein-coding genes (PCGs), 2 rRNAs, and 1 tRNA (tRNA-Met).
The base composition is 30.26% A, 16.44% C, 16.35% G, and 33.95% T, with a G þC content of 35.76%.
According to the phylogenetic analysis, Alcyonacea family are clustered in different clades.
ARTICLE HISTORY
Received 23 December 2018
Accepted 15 January 2019
KEYWORDS
Mitogenome; soft coral;
Sinularia ceramensis;
protein-coding genes;
transfer RNA genes;
ribosomal RNA genes
The genus Sinularia May, 1898 is one of the most pervasive
Indo-Pacific soft corals that has been settled in wide range of
habitats (Fabricius and Alderslade 2001). So far, the complete
mitogenome of two species of Sinularia consisting of
Sinularia peculiaris (JX023274 and NC_018379) and Sinularia
cf. cruciate (KY462727 and NC_034318) have already been
performed. In the present study, the complete mitochondrial
genome of Sinularia ceramensis Verseveldt, 1977
(GenBank: MK292119) was sequenced using next-gener-
ation sequencing.
An individual of S. ceramensis was collected from the
South China Sea (Sanya, Hainan province, China; 18140
5.9300 N, 10922046.4600 E) and stored in Hainan Tropical
Ocean University Museum of Zoology. The specimen was
identified using PuCAs- mtMutS (Benayahu et al. 2018). The
genomic DNA was extracted by Rapid Animal Genomic DNA
Isolation Kit (Sangon Biotech Co., Ltd., Shanghai, CN; NO.
B518221). A genomic library was constructed followed by
paired-end (2 150 bp) next-generation sequencing, using
the Illumina HiSeq X-ten sequencing platform (Tianjin, China).
Quality checks for sequencing reads were carried out by
FastQC (Andrews 2010) and the sequences were assembled
and mapped to the reference Sinularia mitochondrial gen-
ome (Sinularia peculiaris, JX023274) with Spades v3.9.0
(Bankevich et al. 2012) and bowtie v2.2.9 (Langmead and
Salzberg 2012). Putative tRNA gene was determined using
ARWEN (http://130.235.46.10/ARWEN/) online software. All
genes were annotated based on gene order on the reference
mitochondrial map using BLAST analysis (https://blast.ncbi.
nlm.nih.gov). In addition, to annotate PCGs, the position of
start and stop codons were re-considered.
The complete mitogenome of S. ceramensis was 18,740 bp
in length with 14 protein-coding genes (PCGs), 2 ribosomal
RNAs (rRNAs), and 1 transfer RNA (tRNA-Met). The
overall nucleotide composition of the major strand of the
S. ceramensis mitogenome was as follows: 30.26% A, 16.44%
C, 16.35% G, and 33.95% T, with a total G þC content
of 35.76%.
The tRNA-Met and four protein-coding genes (COX3,ATP6,
ATP8, and COX2) were located on the light strand. All PCGs
began with common ATG start codon. Stop codons included
TAG (ND1,ND6,ND3,ND2,ND5,COX3, and COX2), TAA (CYTB,
ND4L,mutS,ND4,ATP6, and ATP8) and non-complete codons
T- (COX1).
The 12S ribosomal RNA and 16S ribosomal RNA were
encoded on the heavy strand from 1583 to 2633 (1051 bp)
and 9157 to 11124 (1968 bp), respectively, with 12S having a
rather lower A þT content (56.61% vs. 58.49%). The longest
gap but a single overlap were determined between COX2/
COX1 (112 bp) and ND2/ND5 (13 bp), respectively.
The phylogenetic relationship of S. ceramensis among
order Alcyonacea was performed from a concatenated data-
set consisting of the 14 PCGs and 2 rRNAs using the software
MEGA 7.0.26 v. (Kumar et al. 2016) with 1000 bootstrap repli-
cates and GTR model (Figure 1). According to the result,
Alcyoniidae was divided into three separated clades while
families Gorgoniidae, Briareidae, and Coralliidae were placed
between Alcyoniidae clades. A comprehensive taxonomical
CONTACT Pei-Zheng Wang condywpz@126.com; 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. 1, 815816
https://doi.org/10.1080/23802359.2019.1574678
status of Alcyoniidae family needs to revise using whole
mitochondrial genome sequences.
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 a cooperative agreement provided by the
Science and Technology Major Project of Hainan Province under [Grant
ZDKJ2016009-3], Hainan Tropical Ocean University Doctoral Research
Funding [RHDXB201628], Science and Technology Cooperation Fund of
College and Local Government in SanYa City [2017YD01].
ORCID
Alireza Asem http://orcid.org/0000-0002-8991-4903
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Figure 1. Phylogenetic tree showing the relationship among S. ceramensis and other members of order Alcyonacea based on maximum-likelihood (ML) approach.
Numbers behind each node denote the bootstrap support values. The GenBank accession numbers are indicated on the right side of species names.
816 A. ASEM ET AL.
... A phylogenetic analysis of family Alcyoniidae was established 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 contained nine PCGs (published S. glaucum mitogenome lacks nad3, nad4L, nad6, cytb, and mutS) (Beaton et al. 1998). ...
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Fast gapped-read alignment with Bowtie 2
  • B Langmead
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Langmead B, Salzberg S. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods. 9:357-359.