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

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


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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Mitochondrial DNA Part B
ISSN: (Print) 2380-2359 (Online) Journal homepage:
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:
© 2019 The Author(s). Published by Informa
UK Limited, trading as Taylor & Francis
Published online: 24 Oct 2019.
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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
Department of Biology, Chengde Medical University, Chengde, Hebei Province, China;
College of Fisheries and Life Science, Hainan
Tropical Ocean University, Sanya, China;
Department of Chemical Engineering, Chengde Petroleum College, Chengde, China;
of Physiology, Chengde Medical University, Chengde, Hebei Province, China
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.
Received 10 July 2019
Accepted 25 September 2019
Mitogenome; soft coral;
trocheliophorum; base
composition; phylogenetic
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 (
The determination of the putative transfer RNA gene
(tRNAs) was performed by online software ARWEN (http:// and tRNAscan-SE2.0 (http://lowelab.
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 Department of Biology, Chengde Medical University, Chengde 067000, Hebei Province, China;
Weidong Li 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 (, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
2019, VOL. 4, NO. 2, 37343735
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.
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
Alireza Asem
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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.
... 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). ...
Full-text available
The complete mitochondrial genome of Sinularia penghuensis was sequenced and analyzed using next-generation sequencing. The present mitochondrial genome was 18730 bp in length, containing 14 protein-coding genes (PCGs) (cox1-cox3.nad1-nad6, nad4L, atp6, atp8, cytb, and MutS), two ribosomal RNA genes (rRNAs) (12S and 16S), and one transfer RNA gene (Met-tRNA). The phylogenetic analysis of family Alcyoniidae revealed that S. penghuensis and Sinularia maxima cluster together. Five species in Sinularia reveals high identity in mitogenome sequences that the lowest variable sites (SNPs) were found between S. penghuensis and S. maxima.
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Comprising approximately 7500 living species of various corals and sea anemones, Anthozoa ranks among the most ecologically and economically valuable marine taxa. However, the taxonomy and systematics of anthozoans remain in flux as several facets of their biology (e.g. cryptic speciation, hybridisation and introgression, morphological plasticity and convergence) confound taxonomists even today. Rapid advancements in molecular sequencing and analyses have made available vast quantities of genomic data on an increasing number of species across the anthozoan tree of life. While whole genome assemblies are expected to result in the most robust phylogenetic trees, reduced-representation techniques such as genome skimming, RAD-seq, phylotranscriptomics and hybrid capture have led to well-supported inferences at various taxonomic levels and may still be favoured at this stage due to the high cost associated with even a single genome assembly. Here, we examine the different genotyping and analytical approaches used in anthozoan phylogeny reconstructions, their applicability across different divergences, and the coverage of studies among anthozoan clades to date. Based on our review of 82 phylogenomic studies, we describe the suitability of methods employed relative to their aims, highlight the imbalanced coverage of taxonomic groups studied and assess immediate and long-term needs where consolidation and streamlining of approaches would further advance the field. Overall, we find that Scleractinia (Anthozoa) is the most phylogenetically sampled group and studies on Octocorallia (Anthozoa) and its subclades are emerging. Nevertheless, we emphasise the need for more phylotranscriptomic, hybrid capture and whole genome sequencing across all anthozoans to increase topological support and generate more precise divergence time estimates. The enhanced phylogenetic understanding of Anthozoa is expected to provide insights into the evolution of genes and adaptations to environmental stressors amidst the current climate and mass extinction crises.
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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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Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density and content, gene orders, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5’ and/or 3’ untranslated regions (UTRs) of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, mtMutS, was found to undergo alternative polyadenylation (APA), and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. Conclusions: Mt-mRNA processing in octocorals bearing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represents a first step towards understanding its functional and evolutionary implications.
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We use full mitochondrial genomes to test the robustness of the phylogeny of the Octocorallia; to determine the evolutionary pathway for the five known mitochondrial gene rearrangements in octocorals; and to test the suitability of using mitochondrial genomes for higher taxonomic level phylogenetic reconstructions. Our phylogeny supports three major divisions within the Octocorallia and show that Paragorgiidae is paraphyletic, with Sibogagorgia forming a sister branch to the Coralliidae. Furthermore, Sibogagorgia cauliflora has what is presumed to be the ancestral gene order in octocorals, but the presence of a pair of inverted repeat sequences suggest that this gene order was not conserved but rather evolved back to this apparent ancestral state. Based on this we recommend the resurrection of the family Sibogagorgiidae to fix the paraphyly of the Paragorgiidae. This is the first study to show that in the Octocorallia, mitochondrial gene orders have evolved back to an ancestral state after going through a gene rearrangement, with at least one of the gene orders evolving independently in different lineages. A number of studies have used gene boundaries to determine the type of mitochondrial gene arrangement present. However our findings suggest that this method known as gene junction screening may miss evolutionary reversals. Additionally, substitution saturation analysis demonstrates that while whole mitochondrial genomes can be used effectively for phylogenetic analyses within Octocorallia, their utility at higher taxonomic levels within Cnidaria is inadequate. Therefore for phylogenetic reconstruction at taxonomic levels higher than subclass within the Cnidaria, nuclear genes will be required, even when whole mitochondrial genomes are available. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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This paper describes five new species of the soft coral genus Sarcophyton which were identified by their morphological characters (colony form and sclerite shape). The five species have been named: S. aalbersbergi sp. nov., S. aldersladei sp. nov., S. alexanderi sp. nov., S. skeltoni sp. nov and S. soapiae sp. nov. For the first time it is documented that there is a Sarcophyton species that does not have sclerites in the interior of the disc.