Content uploaded by Junjie Wang
Author content
All content in this area was uploaded by Junjie Wang on Nov 04, 2022
Content may be subject to copyright.
Gene 820 (2022) 146232
Available online 31 January 2022
0378-1119/© 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
Novel duplication remnant in the rst complete mitogenome of Hemitriakis
japanica and the unique phylogenetic position of family Triakidae
Chen Wang
a
,
1
, Tinghe Lai
c
,
1
, Peiyuan Ye
d
, Yunrong Yan
e
, Pierre Feutry
f
, Binyuan He
c
,
Zhongjian Huang
c
, Ting Zhu
c
, Junjie Wang
b
,
*
, Xiao Chen
a
,
g
,
*
a
College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
b
Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
c
Guangxi Academy of Oceanography, Nanning 530000, China
d
College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
e
College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
f
CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
g
Guangxi Mangrove Research Center, Beihai 536000, China
ARTICLE INFO
Edited by: Xavier Carette
Keywords:
Hemitriakis japanica
Mitogenome
Duplication remnant
Gene rearrangement
Tandem duplication/random loss
Intramitochondrial recombination
Phylogenetic analyses
ABSTRACT
In this study, we rstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica),
which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The
mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA
genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and
tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and
latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tan-
demly duplicated twice while accompanied by being deleted once at least. This is the rst report of mitogenomic
gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and
maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In
summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged
process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
1. Introduction
Mitochondria are two-layer membrane coated respiratory organ-
elles, which are thought to be obtained from Alphaproteobacteria
through endosymbiosis, and act as the energy factories existing in most
eukaryotic cells (Henze and Martin, 2003; Munoz-Gomez et al., 2017).
Mitochondria have their own genome to synthesize proteins autono-
mously and participate in a variety of different physiological functions
in organisms (McBride et al., 2006). After a long period of evolution,
mitochondria retain their own streamlined set of DNA and their genetic
composition is consistent in most metazoa, suggesting these genes are
important for maintaining the basic functions of mitochondria (Brown
et al., 1979). The mitochondrial genome (mitogenome) characteristics
include fast evolution, small molecular weight, simple structure and
maternal inheritance. Therefore, it is used as a reliable marker in cla-
distic systematics (Wolstenholme, 1992; Boore et al., 2000). The typical
sh mitogenome is a 15–20 kb long double-stranded and closed-circular
molecule, containing 13 protein-coding genes (PCGs), two ribosomal
RNA genes (rRNAs), 22 transfer RNA genes (tRNAs) and 2 non-coding
region named the light-strand origin of replication (OL) and the con-
trol region (CR), respectively (Boore, 1999; Jameson et al., 2003). The
mitogenome structure of sh is generally considered to be conservative
and has been widely used to deduce phylogenetic relationships and
population genetics (Wolstenholme, 1992; Satoh et al., 2016).
Shark (Class Chondrichthyes) is one of the most ancient and
advanced lineages of shes and has the most evolutionary distinct
Abbreviations: BI, Bayesian inference; ML, Maximum likelihood; Mitogenome, Mitochondrial genome; tRNA, Transfer RNA; rRNA, Ribosomal RNA; PCG, Protein
coding region.
* Corresponding authors at: College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China (X. Chen).
E-mail addresses: wangjunjie@hotmail.co.jp (J. Wang), chenxiao@scau.edu.cn (X. Chen).
1
These authors contributed equally to this work.
Contents lists available at ScienceDirect
Gene
journal homepage: www.elsevier.com/locate/gene
https://doi.org/10.1016/j.gene.2022.146232
Received 24 November 2021; Received in revised form 22 December 2021; Accepted 18 January 2022
Gene 820 (2022) 146232
2
radiation of all vertebrates (Chen et al., 2013; Stein et al., 2018). They
have radiated throughout the world’s oceans and dominated upper
trophic levels in their 420-million-year history (Dulvy et al., 2021; Dulvy
and Reynolds, 1997; Sibert and Rubin, 2021). However, extinction risk
of sharks has been determined for the entire clade by rst global IUCN
Red List of Threatened Species assessment (Dulvy et al., 2014). As an
excellent molecular tool, the mitogenome has been widely used in
population genetics and phylogeny studies of sharks. However, to date,
the mitogenome of only 56 shark species have been sequenced, repre-
senting about 10% of all shark species (Ebert et al., 2021). Therefore,
more information on shark mitochondrial genomes is needed to explore
their evolution.
The Japanese topeshark (Hemitriakis japanica) belongs to the family
Triakidae (Carcharhiniformes), which comprises 9 genera and 46 spe-
cies. It is widely distributed in the subtropical waters of China, southern
Korea and Japan (Compagno et al., 1998). Hemitriakis japanica usually
lives inshore and offshore down to at least 100 m depth. It is
ovoviviparous and the embryos feed solely on yolk (Dulvy and Reynolds,
1997). Adults are generally 82–102 cm long, with a maximum recorded
size of 110 cm (Compagno et al., 1984). Due to being captured for food
and climate change, Hemitriakis japanica has undergone a population
reduction of 50–79% over the past three decades (30 years), and been
assessed as Endangered A2d on the IUCN Red List in 2021 (Simpfen-
dorfer and Dulvy, 2017; Walls et al., 2021). In order to increase
knowledge about the evolution of this threatened shark, we rst deter-
mined the complete mitochondrial genome of H. japonica and analysed
its phylogenetic position basing on the mitogenomic data. Finally, to ll
the gap in genetic information, we chose 51 mitogenomes of Carch-
arhiniformes species to reconstructed phylogenetic tree with two Lam-
niformes species as outgroups (Table 1). Within Carcharhiniformes, only
the mitogenomes of H. japanica and S. torazame have shown gene
rearrangement so far. Based on two type of gene rearrangements, the
possibly rearranged processes were analyzed and contributed further
insight into shark mitogenomes evolution and phylogeny.
Table 1
List of Carcharhiniformes species and two outgroups used in this paper.
Family Species Size (bp) AT% Genbank Reference
Carcharhinidae Carcharhinus acronotus 16,719 61.6 NC_024055 (Yang et al., 2016)
Carcharhinus albimarginatus 16,706 61.4 NC_047239 –
Carcharhinus amblyrhynchoides 16,705 61.8 NC_023948 (Feutry et al., 2016)
Carcharhinus amblyrhynchos 16,705 61.6 NC_047238 (Dunn et al., 2020)
Carcharhinus amboinensis 16,704 62.0 NC_026696 (Feutry et al., 2016)
Carcharhinus brachyurus 16,704 61.7 NC_057525 (Kim et al., 2021)
Carcharhinus brevipinna 16,706 61.4 NC_027081 (Chen et al., 2016)
Carcharhinus falciformis 16,677 61.4 NC_042256 (Johri et al., 2019)
Carcharhinus leucas 16,704 62.6 NC_023522 (Chen et al., 2015)
Carcharhinus limbatus 16,705 61.7 NC_057057 –
Carcharhinus longimanus 16,706 61.5 NC_025520 (Li et al., 2014)
Carcharhinus macloti 16,701 60.8 NC_024862 (Chen et al., 2016)
Carcharhinus melanopterus 16,706 61.4 NC_024284 (Chen et al., 2016)
Carcharhinus obscurus 16,706 61.5 NC_020611 (Blower et al., 2013)
Carcharhinus perezii 16,709 61.5 MW528216 –
Carcharhinus plumbeus 16,706 61.2 NC_024596 (Blower and Ovenden, 2016)
Carcharhinus sorrah 16,707 61.0 NC_023521 (Chen et al., 2015)
Carcharhinus tjutjot 16,705 60.6 NC_026871 (Chen et al., 2016)
Galeocerdo cuvier 16,703 63.1 NC_022193 (Chen et al., 2014)
Glyphis fowlerae 16,704 60.6 NC_028342 (Li et al., 2015)
Glyphis garricki 16,702 60.8 NC_023361 (Feutry et al., 2015)
Glyphis glyphis 16,701 61.0 NC_021768 (Chen et al., 2014)
Lamiopsis temminckii 16,708 61.1 NC_028341 (Li et al., 2015)
Lamiopsis tephrodes 16,705 61.2 NC_028340 (Li et al., 2015)
Loxodon macrorhinus 16,702 61.1 NC_029843 (Wang et al., 2016)
Prionace glauca 16,705 62.5 NC_022819 (Chen et al., 2015)
Rhizoprionodon acutus 16,693 63.0 NC_046016 (Liu et al., 2020)
Scoliodon laticaudus 16,695 63.1 NC_042504 (Periasamy et al., 2016)
Scoliodon macrorhynchos 16,693 63.1 NC_018052 (Chen et al., 2014)
Triaenodon obesus 16,700 61.1 NC_026287 (Chen et al., 2016)
Hemigaleidae Hemigaleus microstoma 16,701 60.1 NC_029400 (Mai et al., 2016)
Hemipristis elongata 16,691 63.0 NC_032065 (Huang et al., 2016)
Proscylliidae Proscyllium habereri 16,708 62.1 NC_030216 (Chen et al., 2016)
Pseudotriakida
Pseudotriakis microdon 16,700 63.6 NC_022735 (Tanaka et al., 2013)
Cephaloscyllium fasciatum 16,703 61.9 MZ424309 –
Cephaloscyllium umbratile 16,698 62.1 NC_029399 (Chen et al., 2016)
Galeus melastomus 16,706 63.2 NC_049881 –
Halaelurus buergeri 19,100 61.1 NC_031811 (Chen et al., 2016)
Parmaturus melanobranchus 16,687 62.5 NC_056784 –
Poroderma pantherinum 16,686 61.1 NC_043830 (van Staden et al., 2018)
Scyliorhinidae Scyliorhinus canicula 16,697 62.0 NC_001950 (Delarbre et al., 1998)
Scyliorhinus torazame 17,861 61.8 AP019520 (Hara et al., 2018)
Sphyrnidae
Eusphyra blochii 16,727 61.3 NC_031812 (Feutry et al., 2016)
Sphyrna lewini 16,726 60.5 NC_022679 (Chen et al., 2015)
Sphyrna mokarran 16,719 61.4 NC_035491 (Ruck et al., 2017)
Sphyrna tiburo 16,723 60.7 NC_028508 (Díaz-Jaimes et al., 2016)
Sphyrna zygaena 16,731 61.7 NC_025778 (Bolano-Martinez et al., 2016)
Triakidae Hemitriakis japanica 17,301 60.0 KJ617039 This study
Mustelus griseus 16,754 61.0 NC_023527 (Chen et al., 2016)
Mustelus manazo 16,707 61.8 NC_000890 (Cao et al., 1998)
Mustelus mustelus 16,755 60.8 NC_039629 (Hull et al., 2018)
Outgroups Chiloscyllium griseum 16,755 63.9 NC_017882 –
Lamna ditropis 16,702 61.1 NC_024269 (Chang et al., 2014)
C. Wang et al.
Gene 820 (2022) 146232
3
2. Materials and methods
2.1. Specimen collection, DNA extraction, PCR amplication and
sequencing
One specimen of H. japanica was collected from Weizhou Island,
Guangxi Province, China. The specimen was preserved in the South
China Agriculture University (voucher GXWZ20130921-14). All exper-
iments were conducted in accordance with the guidelines and approval
of the Animal Research and Ethics Committees of South China Agri-
cultural University (SCAU). DNA was extracted from the muscle using
the Marine Animal Tissue Genomic DNA Extraction Kit (DP324). And
the Takara
TM
LA-Taq DNA polymerase kit was used to amplify the seg-
ments. To ensure maximum DNA amplication, the parameters of the
PCR reactions were mostly in accordance with the manufacturer’s rec-
ommendations. The nine fragments were amplied using universal
primers for Carcharhiniformes designed based on published sharks
mitogenomes.
2.2. Sequence assembly, annotation and analysis
Sequence data were analyzed and compiled to create complete
mitogenomes using the SeqMan program from DNAStar v7.1 program
(Burland, 2000). Species identication was done based on morpholog-
ical characters and fragments of COI gene downloaded from National
Center of Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih
.gov/genbank/). The mitogenomes were rst annotated with MITOS2
Web Server (Bernt et al., 2013). Then the tRNA genes and their sec-
ondary structures were identied using the tRNAscan-SE Search Server
v2.0 (Lowe and Chan, 2016), then further conrmed with ARWEN v1.2
software using default search mode (Laslett and Canback, 2008).
Annotation and accuracy of boundary determination of 13 protein-
coding and two ribosomal RNA genes assessed through comparison
with other released reference mitogenomes of Carcharhiniformes spe-
cies after manual alignment using DNAman v6.0 (Wang, 2016).
The mitogenome of H. japanica was drawn into full circular genome
using CGView Server v1.0 (Fig. 1) (Grant and Stothard, 2008). The base
compositions, codon usage and relative synonymous codon usage
(RSCU) values were calculated in MEGA X (Kumar et al., 2018), then
drawn using ggblot2 by R. Strand asymmetry was measured on the basis
of the following formulas: AT skew =(A – T) / (A +T) and GC skew =(G
– C) / (G +C) (Perna and Kocher, 1995). And the studied mitogenome
has been uploaded in genbank using the Bankit program under accession
number KJ617039.
2.3. Phylogenetic analyses
At present, 51 complete mitogenomes of Carcharhiniformes species
(only ve Triakidae) have been deposited in NCBI. They were used to
construct the phylogenetic tree (Table 1). Chiloscyllium griseum
(NC_017882) and Lamna ditropis (NC_024269) were used as outgroups.
A partition approach was applied and we distinguished three partitions:
the rst and second codons of 12H-strand encoded PCGs (excluding the
ND6 gene), and the two rRNA genes. The 12 PCGs and rRNAs genes were
aligned by the MACSE v2.03 and MAFFT v7 program (Ranwez et al.,
2018; Katoh and Standley, 2013), respectively. Then, ambiguously
aligned fragments of rRNAs alignments were removed using Gblocks
0.91b (Talavera et al., 20072007). And the nal dataset was created by
Fig. 1. Gene map of the Hemitriakis japanica mitogenome. The outside the outermost circle genes are transcribed clockwise, while the inside the outermost circle
genes are transcribed counterclockwise. The inside circle shows the GC content and GC skewness.
C. Wang et al.
Gene 820 (2022) 146232
4
concatenating the above three segments by Phylosuite v1.2.2 software
(Zhang et al., 2020).
Then, the ModelFinder was used to select the best-t partition model
with the greedy algorithm (Kalyaanamoorthy et al., 2017), and GTR +F
+I +G4 was selected as the optimal model for the 3 partitions according
to BIC criterion. Phylogenetic analyses were performed using Baysian
Inference (BI) and Maximum Likelihood (ML) analyses (Nylander et al.,
20042004; Sitnikova, 1996). Condence in the ML was assessed with
bootstraping using IQ-Tree v1.6.2 (Minh et al., 2020), under 10,000
ultrafast bootstraps with approximate Bayes test. Bayesian inference was
conducted in MrBayes v3.2.6 (Ronquist et al., 2012), under 2 parallel
runs and 2,000,000 generations, the initial 25% of sampled data was
discarded as burn-in with default settings. The iTOL dataset les were
then used to visualize and annotate the phylograms and gene orders in
iTOL v6 (Letunic and Bork, 2016).
3. Results and discussion
3.1. Genome structure, composition and skewness
The complete mitogenome of H. japanica (GenBank Accession No.
KJ617039) was 17,301 base pairs (bp) in length, falling well within the
known range in sharks: 16,677 bp (Carcharhinus falciformis) to 19,100
bp (Halaelurus buergeri). The mitogenomes of H. japanica possessed the
typical genes, including 13 PCGs, 22 tRNAs, two rRNAs (12S and 16S)
and a large CR. Its gene order and transcriptional direction have been
hypothesized for most vertebrates (Fig. 1, Table 2). However, the
mitogenomic organization of H. japanica was found to be different from
that of typical bony sh. Generally, there is no spacer or several base
pairs between the Cytb gene and tRNA-Thr gene. Here, an 824 bp
intergenic region was found between the Cytb and the tRNA-Thr genes,
which is different from other Carcharhiniformes species.
The overall base composition is 31.1% A, 26.7% C, 13.4% G and
28.9 % T, respectively. All mitochondrial genes were biased in nucleo-
tide composition: the AT content is distinctly higher than GC content
(Fig. 2a-b), which is congruent with most sh mitogenomes previously
reported. Interestingly, base composition analysis shows that the H.
japanica mitogenome has the lowest AT content of all those known for
Carcharhiniformes species so far (Table 1). Similar to published shark
mitogenomes (Cao et al., 1998; Chen et al., 2016; Hull et al., 2018), AT-
skews are usually positive and GC-skews are negative. The skewness in
the mitogenome of H. japanica shows AT-skews ranging from −0.36
(ND6) to 0.16 (rRNAs) whereas all the GC-skews are negative except for
the ND6 (0.56) and the tRNAs genes (0.08) (Fig. 2c). The nucleotide
composition is generally regarded as a potential indicator of gene di-
rection and selective pressures during replication and transcription
(Perna and Kocher, 1995; Ferretti et al., 1994).
3.2. Protein coding regions, transfer RNA and ribosomal RNA
The 13 PCGs totaled 11,427 bp in length accounting for 66.05% of
the whole genome and encoding 3,797 amino acids. All PCGs are
Table 2
Annotation of the complete mitogenome of Hemitriakis japanica.
Gene Strand Position Size (bp) codon Anti-codon Intergenic spacer
1
(bp)
From to Star Stop
tRNA-Phe (F) H 1 69 69 GAA 0
12S rRNA H 70 1,021 952 0
tRNA-Val (V) H 1,022 1,093 72 TAC 0
16S rRNA H 1,094 2,762 1,669 0
tRNA-Leu1 (L1) H 2,763 2,837 75 TAA 0
ND1 H 2,838 3,812 975 ATG TAA 0
tRNA-Ile (I) H 3,813 3,882 70 GAT 1
tRNA-Gln (Q) L 3,884 3,955 72 TTG 0
tRNA-Met (M) H 3,956 4,024 69 CAT 0
ND2 H 4,025 5,071 1,047 ATG T- −2
tRNA-Trp (W) H 5,070 5,140 71 TCA 1
tRNA-Ala (A) L 5,142 5,210 69 TGC 0
tRNA-Asn (N) L 5,211 5,283 73 GTT 0
O
L
– 5,289 5,318 30 5
tRNA-Cys (C) L 5,318 5,386 69 GCA −1
tRNA-Tyr (Y) L 5,388 5,457 70 GTA 1
COI H 5,459 7,015 1,557 GTG TAA 0
tRNA-Ser1 (S1) L 7,016 7,086 71 TGA 3
tRNA-Asp (D) H 7,090 7,159 70 GTC 7
COII H 7,167 7,857 691 ATG T- 0
tRNA-Lys (K) H 7,858 7,931 74 TTT 1
ATP8 H 7,933 8,100 168 ATG TAA −10
ATP6 H 8,091 8,774 684 ATG TAA −1
COIII H 8,774 9,559 786 ATG TAA 2
tRNA-Gly (G) H 9,562 9,631 70 TCC 0
ND3 H 9,632 9,982 351 ATG T- −2
tRNA-Arg (R) H 9,981 10,050 70 TCG 0
ND4L H 10,051 10,347 297 ATG TAA −7
ND4 H 10,341 11,721 1,381 ATG T- 0
tRNA-His (H) H 11,722 11,791 70 GTG 0
tRNA-Ser2 (S2) H 11,792 11,858 67 GCT 0
tRNA-Leu2 (L2) H 11,859 11,930 72 TAG 0
ND5 H 11,931 13,760 1,830 ATG TAA −5
ND6 L 13,756 14,277 522 ATG AGA 0
tRNA-Glu (E) L 14,278 14,347 70 TTC 2
Cytb H 14,350 15,495 1,146 ATG TAG 594
tRNA-Thr (T) H 16,090 16,161 72 TGT 2
tRNA-Pro (P) L 16,164 16,232 69 TGG 0
Control region (CR) H 16,233 17,301 1,069 0
1
Intergenic spacer included overlap region and non-coding region.
C. Wang et al.
Gene 820 (2022) 146232
5
encoded by the heavy strand (H-strand) except for the ND6 gene, which
is encoded by the light strand (L-strand). The length of the PCGs ranges
from 168 bp (ATP8) to 1,830 bp (ND5), and they all present a bias in A +
T content (Table 2, Fig. 2b). More specically, the third codon has a
higher A +T content than the other codons (Fig. 2b). The strongest AT-
and GC- skews were the second codon (-0.37) and the third codon
(-0.77) of PCGs, respectively (Fig. 2c). Additionally, the COI gene using
GTG as the initiation codon, the remaining protein-coding genes started
with an ATG codon, which is quite common among sh mitogenomes.
Except for the ND6 gene terminated by a rare AGA codon and the Cytb
gene terminated by the canonical TAG codon, the PCG genes were
stopped by TAA (or incomplete T) codons (Table 2).
The high frequent amino acids (AA) in the mitogenome of H. japanica
were tRNA-Leu1 (12.87%), tRNA-Ile (9.03%) and tRNA-Thr (7.53%),
while the tRNA-Cys (0.61%), tRNA-Ser1 (1.45%) and tRNA-Asp (1.87%)
were rarely used (Fig. 3a). The relative synonymous codon usage (RSCU)
values were calculated for the mitogenome of H. japanica as shown in
Fig. 3b. Similar to the skewness analysis, the RSCU analysis showed that
codons were biased towards using more A/T nucleotides at the third
codon (Fig. 2c, Fig. 3b). Nucleotide compositional asymmetries will
provide insight into the nature of the mutational pressures and variation
acting on compositional patterns and evolutionary in sh mitogenomes
(Perna and Kocher, 1995).
The 22 tRNA genes ranged from 67 bp (tRNA-Ser2) to 75 (tRNA-
Leu1) bp in length and were located between rRNAs and PCGs. The total
length of tRNAs genes is 2,621 bp, accounting for 15.15% of the whole
genome. Fourteen tRNAs are encoded on the H-strand and the remaining
tRNAs are encoded on the L-strand. The tRNAs have a high AT content
(59.8%), and the AT skews is 0.02. All tRNAs have typical cloverleaf
structures and are recognized by tRNAscan-SE online (Lowe and Chan,
2016). The biased usage of A and T nucleotides was reected at the base
composition and skewness of tRNAs (Fig. 2a-c). The 12S and 16S rRNA
Fig. 2. Base composition and skewness of the complete mitogenome of Hemitriakis japanica. Base composition in the mitogenome of H. japanica (a-b). AT- and GC-
skews in the mitogenome of the H. japanica (c).
C. Wang et al.
Gene 820 (2022) 146232
6
Fig. 3. Amino acid composition in the mitogenome of Hemitriakis japanica (a); relative synonymous codon usage (RSCU) in the mitogenome of H. japanica (b).
Fig. 4. Sequence alignment of non-coding region (NC) and two genes (tRNA-Thr and Cytb genes). Alignment of NC
60
and tRNA-Thr gene (a); alignment of NC
534
and
partial Cytb gene (b); alignment of NC
13
, partial tRNA-Thr and Cytb genes (c). The NC
60
indicates the partial 5′-NC, NC
534
indicates the other part of NC and NC
13
indicates the partial 5′-NC
594
genes. The dots (.) indicate alignment gaps.
C. Wang et al.
Gene 820 (2022) 146232
7
genes are 1,021 bp and 2,762 bp, respectively. They are located between
tRNA-Phe and tRNA-Leu1 (UUA), and separated by tRNA-Val, similar to
most sh mitogenomes. The rRNAs have a high AT content (60.2%) and
a positive AT-skews (0.16) (Fig. 2).
3.3. Overlaps and non-coding regions
There are 28 bp short intergenic spaces, which are located in 12 gene
junctions and one (ND1-Ile, ND2-Trp, Cys-Tyr, COII-Lys) to seven bp
(Ser1-Asp). Multiple overlaps between adjacent genes were detected and
31 bp overlaps located in nine gene junctions ranging one (ATP8-ATP6)
to 10 bp (Lys-ATP8). The O
L
in the H. japanica mitogenome is 30 bp in
length, located between the tRNA-Trp and the tRNA-Cys genes and
folding into a stem-and-loop secondary structure (Fig. 1). The CR is
1,069 bp long and is located between the tRNA-Pro and the tRNA-Phe.
The AT content of the CR is 67.4% higher than the GC content, with a
slightly negative AT-skew (-0.02).
A 594 bp-long non-coding region (NC
594
) locating between the Cytb
and the tRNA-Thr genes, was detected as a duplication remnant of the
form and the latter genes. Sequence alignment for the genes in
H. japanica mitogenome showed that the NC
594
is highly similar to parts
of the tRNA-Thr and Cytb genes (Fig. 4). The NC
594
was composed of two
parts, a 60 bp fragment (NC
60
) at the 5′-end of NC
594
is highly similar to
tRNA-Thr (77.33%) (Fig. 4a), and a 534 bp fragment (NC
534
) at the 3′-
end of NC
594
is highly similar to the partial sequence of the 3′-end Cytb
(83.48%) (Fig. 4b). The partial 5′-NC
534
(NC
13
) is similar to the 3′
sequence of tRNA-Thr gene and the 5′sequence of Cytb’ gene (Fig. 4c).
Therefore, we speculated that NC
594
originated from Cytb gene and
tRNA-Thr gene, which experienced copying and deleting and lost their
function. A similar hypothesis has been proposed in other sh mitoge-
nomes (Chang et al., 2014; Xu et al., 2021; Kong et al., 2009).
3.4. Novel gene order in H. Japanica mitogenome
Our research found a novel duplication remnant occurred in the
complete mitogenome of H. japonica. It is the second time a gene rear-
rangement is found in Carcharhiniformes. The rst one, found in Scy-
liorhinus torazame, consisted of two D-loop regions located in the similar
region of the mitogenome (Hara et al., 2018). In H. japonica, there is a
long intergenic spacer located between the Cytb and the tRNA-Thr genes
(Fig. 5). It’s only the second time gene rearrangement is found in
Carcharhiniformes, and the pattern described here is different to the one
previously reported. Similarly, two type mitochondrial gene arrange-
ments were reported in atshes, genus Cynoglossus, with unique Glu-
Ile-Met (QIM) and Ile-Met-Glu (IMQ) gene arrangements that differed
from the traditional Ile-Glu-Met (IQM) (Wang et al., 2020; Wang et al.,
2020; Gong et al., 2020).
In addition, the mitogenome of the goblin shark Mitsukurina owstoni
(EU528659) (Lamniformes) has a 1,060 bp putative duplication
remnant locating between tRNA-Thr and tRNA-Pro genes. Therefore, it
suggests the Cytb-Thr-Pro-CR may be a gene rearrangement hotspot in
shark mitogenomes, similar to WANCY tRNA clusters characterized by
translocation in teleost (Gong et al., 2020). Gene rearrangement in
vertebrate is mainly caused by mitochondrial mutations, the phenom-
enon can be explained by either the tandem duplication and random loss
(TDRL) or the intramitochondrial recombination models of gene order
rearrangement in vertebrate mitogenomes (Boore et al., 2000; Xu et al.,
2021; San Mauro et al., 20062006; Dowton and Campbell, 2001). The
TDRL model is possibly the most widely accepted a hypothesis to explain
the gene rearrangements in vertebrate mitogenomes (Xu et al., 2021; Lü
et al., 2019; Zhang et al., 2021). It assumes that tandem duplication of
some genes is an important step in the rearrangement events, which
forms a continuously duplicated gene block and subsequent random loss
leads to the non-coding regions between genes. Then these regions
recombine to form the nal mitogenome.
Fig. 5. Inferred pathway of gene rearrangement in the mitogenome of Hemitriakis japanica. Inferred gene rearrangement between the gene order of typical verte-
brates and the mitogenome of H. japanica. The ancestral vertebrate gene order (a); inferred intermediate processes of gene rearrangement (b-d); the gene order in the
mitogenome of H. japanica (e).
C. Wang et al.
Gene 820 (2022) 146232
8
3.5. Inferred pathway of gene rearrangement
Based on the TDRL and intramitochondrial recombination model, we
speculate that the rearrangement process in the mitogenome of
H. japanica is as follows. First of all, the Cytb and the tRNA-Thr gene
tandemly duplicated (Fig. 3b), underwent a complete copy forming the
Cytb-Thr-Cytb’-Thr’ dimeric block in its original position (Fig. 3c). Then
a random deletion occurred in the region, resulting in the redundant
fragments of the Cytb’ and the tRNA-Thr genes being lost. Finally, the
remaining fragments were recombined (Fig. 3d). Two genes lost their
function and recombined into a non-coding region (partial tRNA-Thr
and Cytb’ genes) (Fig. 3e). Considering the NC is 594 bp in length, it is
reasonable to suppose it might be generated from the above pathway.
Furthermore, we found the long non-coding (NC) region of mitoge-
nome in H. japanica is similar to the former Cytb gene (83.48%) and the
latter tRNA-Thr gene (77.33%), and the 3′sequence of the tRNA-Thr
gene and the 5′sequence of Cytb’ are highly semblable (Fig. 4c). It
supported the hypothesis that the large intergenic gap originated from
the duplicated tRNA-Thr and Cytb genes. The random loss region may
occur in 3′-end of the tRNA-Thr gene, or only 5′-Cytb’ gene was deleted.
It may be the reason why random loss and recombination occurred in
this region and the mitogenome of H. japanica has a long duplication
remnant compared to the ancestral vertebrates (Fig. 5).
Based on current technology and methods, it is not possible to
determine accurately the loss position. Simultaneously, the process of
random loss may not be completely random and have a certain selec-
tivity. The specic gene loss sites may not be in the showed position
which selected for the convenience of demonstration.
3.6. Phylogenetic analysis
To test the monophyly and the phylogenetic position of Triakidae
family, and to understand the evolutionary relationships of H. japonica
within the Carcharhiniformes, a phylogenetic tree was reconstructed
based on of BI and ML methods (Fig. 6). Due to the limited published
mitogenomic data, this analysis only includes 7 families (Carcharhini-
dae, Hemigaleidae, Proscylliidae, Pseudotriakidae, Scyliorhinidae,
Sphyrnidae and Triakidae) and 51 species of Carcharhiniformes, of
which only 4 species from two genera belongs to the Triakidae family.
The topologies of the ML and BI trees were consistent and well
Fig. 6. Phylogenetic tree of Carcharhiniformes species was performed using partial genomes, with Bayesian analyses and Maximum likelihood analyses. Species in
red indicates sequence generated in this study. Bootstrap support (left) and bayesian posterior probability (right) values of each clade are displayed next to the nodes
excluding lower than 50 (-).
C. Wang et al.
Gene 820 (2022) 146232
9
supported. The BI posterior probability and ML bootstrap values sup-
porting most clades are high and generally similar. In some clades, the
ML values are lower than those of BI (Fig. 6). The bootstrap support
values of two clades are low (<50%), while the Bayesian posterior
probability is higher than 60%.
The phylogenetic tree showed that Scyliorhinidae, Triakidae and
Carcharhinidae were non-monophyletic, different from previous results
(Hull et al., 2018; van Staden et al., 2018; Wang et al., 2016; Mai et al.,
2016; Huang et al., 2016; Feutry et al., 2016). Hemitriakis japonica
clustered to a main clade including Hemigaleidae; Sphyrnidae and
Carcharhinidae instead of the genus Mustelus in Triakidae. Three species
in Scyliorhinidae clustered with the other families. All species of
Carcharhinidae clustered together and was placed as sister to Sphyrni-
dae except Galeocerdo cuvier, which clustered a main clade including
Sphyrnidae and other Carcharhinidae species. High support values (BI
and ML) for these clades suggest that these results are reliable.
Due to the limited number of species with available mitogenomic
sequences in Carcharhiniformes, we can’t reconstruct the complete
phylogenetic tree including all species of this order in this study. How-
ever, the results show many inconsistencies in the phylogenetic position
of some species with the traditional views. Because the mitogenome
contained more evolutional information, it could reconstruct more
reliable phylogenetic relationship than previous studies using single or
partial gene, and clear up the morphlogical confusion caused by
convergent evolution.
Furthermore, the two sharks in Carcharhiniformes (H. japonica and
S. torazame) presenting mitochondrial gene rearrangements belongs to
different clade. It suggests the two similar mitochondrial gene rear-
rangement events likely occurred independently according to evolu-
tionary parsimony, instead of a gene rearrangement event occurred in a
common ancestor and preserved in H. japonica and S. torazame mean-
while their relatives revert to the typical mitochondrial gene
arrangement.
4. Conclusions
In this study, we sequenced and described the complete mitogenome
of H. japanica, which is 17,301 base pairs (bp) in length with the typical
gene number, order and transcriptional direction of vertebrates. Inter-
estingly, a 594 bp-long non-coding region was found between the Cytb
and the tRNA-Thr genes. Evidence suggests it is a remnant of the Cytb
and tRNA-Thr genes, suitably explained by the tandem duplication/
random loss (TDRL) and mitochondrial recombination mechanisms. The
phylogenetic trees reconstructed using BI and ML methods were
consistent in topology with most nodes well supported. The results
suggest that Scyliorhinidae, Triakidae and Carcharhinidae are non-
monophyletic and H. japonica may be inaccurately categorized to Tri-
akidae with current mitogenome data.
The novel rearrangement pattern provides insight into the mecha-
nisms and illustrates an intermediate process of gene rearrangement in
sh mitogenomes. The mitogenome sequencing of additional shark
species in the future will enable to clarify the phylogenetic relationships
within this group and the status of the Triakidae family and H. japanica
in particular.
Funding
This research was funded by Science and Technology Major Special
Project of Guangxi (GKAA17129002), National Natural Science Foun-
dation of China (41666008), Natural Science Foundation of Guangxi
Province (2016GXNSFDA380035) and Science and Technology Plan
Projects of Guangdong Province, China (2018B030320006).
Institutional Review Board Statement
The study was conducted and approved by the Animal Research and
Ethics Committees of South China Agricultural University, Guangzhou,
China.
CRediT authorship contribution statement
Chen Wang: Software, Validation. Tinghe Lai: Formal analysis.
Peiyuan Ye: Writing – original draft. Yunrong Yan: Funding acquisi-
tion. Pierre Feutry: . Binyuan He: Investigation. Zhongjian Huang:
Resources. Ting Zhu: Data curation. Junjie Wang: Supervision. Xiao
Chen: Conceptualization, Methodology.
Declaration of Competing Interest
The authors declare that they have no known competing nancial
interests or personal relationships that could have appeared to inuence
the work reported in this paper.
References
Henze, K., Martin, W., 2003. Evolutionary biology: essence of mitochondria. Nature 426,
127–128.
Munoz-Gomez, S.A., Wideman, J.G., Roger, A.J., Slamovits, C.H., 2017. The Origin of
Mitochondrial Cristae from Alphaproteobacteria. Mol. Biol. Evol. 34, 943–956.
McBride, H.M., Neuspiel, M., Wasiak, S., 2006. Mitochondria: more than just a
powerhouse. Curr. Biol. 16, 551–560.
Brown, W.M., George, M., Wilson, A.C., 1979. Rapid evolution of animal mitochondrial
DNA. Proc. Natl. Acad. Sci. USA 76 (4), 1967–1971.
Wolstenholme, D.R., 1992. Animal Mitochondrial DNA: Structure and Evolution. Int.
Rev. Cytol. 141, 173–216.
J.L. Boore, The Duplication/Random Loss Model for Gene Rearrangement Exemplied by
Mitochondrial Genomes of Deuterostome Animals. In: Sankoff D., Nadeau J.H. (eds)
Comparative Genomics. Computational Biology. Kluwer Academic Publishers,
Dordrecht, Netherlands. 1 (2000) 133–147.
Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic. Acids. Res. 27 (8),
1767–1780.
D. Jameson, A.P. Gibson, C. Hudelot, H.P. G., OGRe: a relational database for
comparative analyses of mitochondrial genomes, Nucleic. Acids. Res. 31 (2003)
202–206.
Satoh, T.P., Miya, M., Mabuchi, K., Nishida, M., 2016. Structure and variation of the
mitochondrial genome of shes. BMC Genom. 17, 719.
Chen, X., Ai, W., Ye, L., Wang, X., Lin, C., Yang, S., 2013. The complete mitochondrial
genome of the grey bamboo shark (Chiloscyllium griseum) (Orectolobiformes:
Hemiscylliidae): genomic characterization and phylogenetic application. Acta
Oceanolog. Sin. 32, 59–65.
Stein, R.W., Mull, C.G., Kuhn, T.S., Aschliman, N.C., Davidson, L.N.K., Joy, J.B.,
Smith, G.J., Dulvy, N.K., Mooers, A.O., 2018. Global priorities for conserving the
evolutionary history of sharks, rays and chimaeras. Nat. Ecol. Evol. 2 (2), 288–298.
Dulvy, N.K., Pacoureau, N., Rigby, C.L., Pollom, R.A., Jabado, R.W., Ebert, D.A.,
Finucci, B., Pollock, C.M., Cheok, J., Derrick, D.H., Herman, K.B., Sherman, C.S.,
VanderWright, W.J., Lawson, J.M., Walls, R.H.L., Carlson, J.K., Charvet, P.,
Bineesh, K.K., Fernando, D., Ralph, G.M., Matsushiba, J.H., Hilton-Taylor, C.,
Fordham, S.V., Simpfendorfer, C.A., 2021. Overshing drives over one-third of all
sharks and rays toward a global extinction crisis. Curr. Biol. 31 (22), 5118–5119.
Dulvy, N.K., Reynolds, J.D., 1997. Evolutionary transitions among egg–laying,
live–bearing and maternal inputs in sharks and rays. Proc. Biol. Sci. 264 (1386),
1309–1315.
Sibert, E.C., Rubin, L.D., 2021. An early Miocene extinction in pelagic sharks. Science
372 (6546), 1105–1107.
N.K. Dulvy, S.L. Fowler, J.A. Musick, R.D. Cavanagh, P.M. Kyne, L.R. Harrison, J.K.
Carlson, L.N. Davidson, S.V. Fordham, M.P. Francis, C.M. Pollock, C.A.
Simpfendorfer, G.H. Burgess, K.E. Carpenter, L.J. Compagno, D.A. Ebert, C. Gibson,
M.R. Heupel, S.R. Livingstone, J.C. Sanciangco, J.D. Stevens, S. Valenti, W.T. White,
Extinction risk and conservation of the world’s sharks and rays, Elife. 3 (2014)
e00590.
D.A. Ebert, M. Dando, S. Fowler, Sharks of the World: A Complete Guide[M], Princeton
University Press. (2021).
L.J.V. Compagno, V.H. Niem, Triakidae. Houndsharks, smoothhounds, topes. In K.E.
Carpenter and V.H. Niem (eds.) FAO identication guide for shery purposes. The
Living Marine Resources of the Western Central Pacic. FAO, Rome. (1998)
1297–1304.
L.J.V. Compagno, FAO Species Catalogue. Vol 4: Sharks of the world, Part 2-
Carcharhiniformes. FAO Fisheries Synopsis. 125 (1984) 251–633.
Simpfendorfer, C.A., Dulvy, N.K., 2017. Bright spots of sustainable shark shing. Curr.
Biol. 27 (3), R97–R98.
R.H.L. Walls, C.L. Rigby, D. Derrick, Y.V. Dyldin, K. Herman, H. Ishihara, C.-H. Jeong, Y.
Semba, S. Tanaka, I.V. Volvenko, A. Yamaguchi, Hemitriakis japanica. The IUCN Red
List of Threatened Species. (2021) e.T161507A124497048.
Burland, T.G., 2000. DNASTAR’s Lasergene sequence analysis software, Methods. Mol.
Biol. 132, 71–91.
Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J.,
Middendorf, M., Stadler, P.F., 2013. MITOS: improved de novo metazoan
mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319.
Lowe, T.M., Chan, P.P., 2016. tRNAscan-SE On-line: integrating search and context for
analysis of transfer RNA genes. Nucleic. Acids. Res. 44, 54–57.
C. Wang et al.
Gene 820 (2022) 146232
10
Laslett, D., Canback, B., 2008. ARWEN: a program to detect tRNA genes in metazoan
mitochondrial nucleotide sequences. Bioinformatics 24, 172–175.
W. Wang, The Molecular Detection of Corynespora Cassiicola on Cucumber by PCR Assay
Using DNAman Software and NCBI, in: Computer and Computing Technologies in
Agriculture IX. (2016) 248–258.
Grant, J.R., Stothard, P., 2008. The CGView Server: a comparative genomics tool for
circular genomes, Nucleic. Acids. Research. 36, 181–184.
Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K., 2018. MEGA X: Molecular
Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 35,
1547–1549.
Perna, N.T., Kocher, T.D., 1995. Patterns of nucleotide composition at fourfold
degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41 (3), 353–358.
Ranwez, V., Douzery, E.J.P., Cambon, C., Chantret, N., Delsuc, F., 2018. MACSE v2:
Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop
Codons. Mol. Biol. Evol. 35, 2582–2584.
Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7:
improvements in performance and usability. Mol. Biol. Evol. 30 (4), 772–780.
G. Talavera, J. Castresana, Improvement of phylogenies after removing divergent and
ambiguously aligned blocks from protein sequence alignments, Syst. Biol. 56 (2007)
564–577.
D. Zhang, F. Gao, I. Jakovli´
c, H. Zou, J. Zhang, Wei.X. Li, and Gui.T. Wang., PhyloSuite:
An integrated and scalable desktop platform for streamlined molecular sequence
data management and evolutionary phylogenetics studies, Mol. Ecolo. Res. 20
(2020) 348–355.
Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S., 2017.
ModelFinder: fast model selection for accurate phylogenetic estimates. Nat.
Methods. 14, 587–589.
J.A. Nylander, F. Ronquist, J.P. Huelsenbeck, J.L. Nieves-Aldrey, Bayesian phylogenetic
analysis of combined data, Syst. Biol. 53 (2004) 47–67.
Sitnikova, T., 1996. Bootstrap method of interior-branch test for phylogenetic trees. Mol.
Biol. Evol. 13 (4), 605–611.
Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams, M.D., von
Haeseler, A., Lanfear, R., 2020. IQ-TREE 2: New Models and Efcient Methods for
Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37, 1530–1534.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Hohna, S.,
Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efcient
Bayesian phylogenetic inference and model choice across a large model space. Syst.
Biol. 61, 539–542.
Letunic, I., Bork, P., 2016. Interactive tree of life (iTOL) v3: an online tool for the display
and annotation of phylogenetic and other trees. Nucleic. Acids. Res. 44, 242–245.
Cao, Y., Waddell, P.J., Norihiro, O., Masami, H., 1998. The Complete Mitochondrial DNA
Sequence of the Shark Mustelus manazo: Evaluating Rooting Contradictions to Living
Bony Vertebrates. Mol. Biol. Evol. 15, 1637–1646.
Chen, X., Peng, Z., Pan, L., Shi, X., Cai, L., 2016. Mitochondrial genome of the spotless
smooth-hound Mustelus griseus (Carcharhiniformes: Triakidae). Mitochondrial DNA
A DNA Mapp Seq Anal. 27, 78–79.
Hull, K.L., Maduna, S.N., Bester-van der Merwe, A.E., 2018. Characterization of the
complete mitochondrial genome of the common smoothhound shark, Mustelus
mustelus (Carcharhiniformes: Triakidae). Mitochondrial DNA B Resour. 3 (2),
962–963.
Ferretti, V., Lang, B.F., Sankoff, D., 1994. Skewed Base Compositions, Asymmetric
Transition Matrices, and Phylogenetic Invariants. J. Comput. Biol. 1 (1), 77–92.
Chang, C.-H., Shao, K.-T., Lin, Y.-S., Ho, H.-C., Liao, Y.-C., 2014. The complete
mitochondrial genome of the big-eye thresher shark, Alopias superciliosus
(Chondrichthyes, Alopiidae). Mitochondrial DNA. 25 (4), 290–292.
Xu, X.D., Guan, J.Y., Zhang, Z.Y., Cao, Y.R., Storey, K.B., Yu, D.N., Zhang, J.Y., 2021.
Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises
(Mantodea: Mantidae): Translocation, duplication and pseudogenization. Int. J. Biol.
Macromol. 185, 403–411.
Kong, X., Dong, X., Zhang, Y., Shi, W., Wang, Z., Yu, Z., 2009. A novel rearrangement in
the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region
translocation and a tRNA gene inversion. Genome. 52, 975–984.
Hara, Y., Yamaguchi, K., Onimaru, K., Kadota, M., Koyanagi, M., Keeley, S.D.,
Tatsumi, K., Tanaka, K., Motone, F., Kageyama, Y., Nozu, R., Adachi, N.,
Nishimura, O., Nakagawa, R., Tanegashima, C., Kiyatake, I., Matsumoto, R.,
Murakumo, K., Nishida, K., Terakita, A., Kuratani, S., Sato, K., Hyodo, S., Kuraku, S.,
2018. Shark genomes provide insights into elasmobranch evolution and the origin of
vertebrates. Nat. Ecol. Evol. 2 (11), 1761–1771.
Wang, C., Liu, M., Tian, S., Yang, C., Chen, X., 2020. The complete mitochondrial
genome of Cynoglossus roulei (Pleuronectiformes: Cynoglossidae): novel
rearrangement and phylogenetic position analysis. Mitochondrial DNA Part B. 5,
1439–1440.
Wang, C., Chen, H., Tian, S., Yang, C., Chen, X., 2020. Novel Gene Rearrangement and
the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the
Envolution of the Family Cynoglossidae (Pleuronectiformes). Int. J. Mol. Sci. 21
(18), 6895. https://doi.org/10.3390/ijms21186895.
Gong, L., Lu, X., Luo, H., Zhang, Y., Shi, W., Liu, L., Lu, Z., Liu, B., Jiang, L., 2020. Novel
gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome:
New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int. J. Biol.
Macromol. 149, 1232–1240.
D. San Mauro, D.J. Gower, R. Zardoya, M. Wilkinson, A hotspot of gene order
rearrangement by tandem duplication and random loss in the vertebrate
mitochondrial genome, Mol. Biol. Evol. 23 (2006) 227–234.
M. Dowton, N.J.H. Campbell, Intramitochondrial recombination-is it why some
mitochondrial genes sleep_around?, Trends in Ecology and Evolution. 16 (2001)
269–271.
Lü, Z., Zhu, K., Jiang, H., Lu, X., Liu, B., Ye, Y., Jiang, L., Liu, L., Gong, L.i., 2019.
Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene
order and phylogenetic relationships of Anguilliformes. Int. J. Biol. Macromol. 135,
609–618.
Zhang, K., Sun, J., Xu, T., Qiu, J.-W., Qian, P.-Y., 2021. Phylogenetic Relationships and
Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes. Int. J. Mol.
Sci. 22 (4), 1900. https://doi.org/10.3390/ijms22041900.
van Staden, M., Gledhill, K.S., Rhode, C., Bester-van der Merwe, A.E., 2018. The
complete mitochondrial genome and phylogenetic position of the leopard catshark
Poroderma pantherinum. Mitochondrial DNA B Resour. 3 (2), 750–752.
Wang, J., Chen, H., Lin, L., Ai, W., Chen, X., 2016. Mitochondrial genome and
phylogenetic position of the sliteye shark Loxodon macrorhinus. Mitochondrial DNA
A DNA Mapp Seq Anal. 27, 4288–4289.
Mai, Q., Li, W., Chen, H., Ai, W., Chen, X., 2016. Complete mitochondrial genome and
phylogenetic position of the Sicklen weasel shark Hemigaleus microstoma.
Mitochondrial DNA A DNA Mapp Seq Anal. 27, 3491–3492.
Huang, X., Yu, J., Chen, H., Chen, X., Wang, J., 2016. Complete mitochondrial genome
and the phylogenetic position of the snaggletooth shark Hemipristis elongata
(Carcharhiniformes: Hemigaleidae). Mitochondrial DNA B Resour. 1 (1), 538–539.
Feutry, P., Kyne, P.M., Chen, X., 2016. The phylogenomic position of the Winghead
Shark Eusphyra blochii (Carcharhiniformes, Sphyrnidae) inferred from the
mitochondrial genome. Mitochondrial DNA B Resour. 1 (1), 386–387.
Yang, L., Matthes-Rosana, K.A., Naylor, G.J., 2016. Complete mitochondrial genome of
the blacknose shark Carcharhinus acronotus (Elasmobranchii: Carcharhinidae).
Mitochondrial DNA A DNA Mapp Seq Anal. 27, 169–170.
Feutry, P., Pillans, R.D., Kyne, P.M., Chen, X., 2016. Complete mitogenome of the
Graceful Shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA A DNA Mapp Seq Anal. 27, 314–315.
Dunn, N., Johri, S., Curnick, D., Carbone, C., Dinsdale, E.A., Chapple, T.K., Block, B.A.,
Savolainen, V., 2020. Complete mitochondrial genome of the gray reef shark,
Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae). Mitochondrial
DNA B Resour. 5 (3), 2080–2082.
Feutry, P., Every, S.L., Kyne, P.M., Sun, R., Chen, X., 2016. Complete mitochondrial
genome of the Pigeye Shark Carcharhinus amboinensis (Carcharhiniformes:
Carcharhinidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27, 2129–2130.
Kim, S.W., Park, S.Y., Kwon, H., Giri, S.S., Kim, S.G., Kang, J.W., Kwon, J., Lee, S.B.,
Jung, W.J., Lee, J., Park, S.C., Kim, J.H., 2021. Complete mitochondrial genome and
phylogenetic analysis of the copper shark Carcharhinus brachyurus (Gunther, 1870).
Mitochondrial DNA B Resour. 6, 1659–1661.
Chen, X., Xiang, D., Peng, X., Ai, W., Chen, H., 2016. The complete mitochondrial
genome of the spinner shark Carcharhinus brevipinna. Mitochondrial DNA A DNA
Mapp Seq Anal. 27, 1666–1667.
Johri, S., Solanki, J., Cantu, V.A., Fellows, S.R., Edwards, R.A., Moreno, I., Vyas, A.,
Dinsdale, E.A., 2019. ’Genome skimming’ with the MinION hand-held sequencer
identies CITES-listed shark species in India’s exports market. Sci. Rep. 9, 4476.
Chen, X., Liu, M., Peng, Z., Shi, X., 2015. Mitochondrial genome of the bull shark
Carcharhinus leucas (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. 26
(6), 813–814.
Li, W., Dai, X., Xu, Q., Wu, F., Gao, C., Zhang, Y., 2014. The complete mitochondrial
genome sequence of Oceanic whitetip shark, Carcharhinus longimanus
(Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. 26, 1–2.
Chen, X., Liu, M., Xiao, J., Yang, W., Peng, Z., 2016. Complete mitochondrial genome of
the hardnose shark Carcharhinus macloti (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA A DNA Mapp Seq Anal. 27, 1090–1091.
Chen, X., Shen, X.J., Arunrugstichai, S., Ai, W., Xiang, D., 2016. Complete mitochondrial
genome of the blacktip reef shark Carcharhinus melanopterus (Carcharhiniformes:
Carcharhinidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27, 873–874.
Blower, D.C., Hereward, J.P., Ovenden, J.R., 2013. The complete mitochondrial genome
of the dusky shark Carcharhinus obscurus. Mitochondrial DNA. 24 (6), 619–621.
Blower, D.C., Ovenden, J.R., 2016. The complete mitochondrial genome of the sandbar
shark Carcharhinus plumbeus. Mitochondrial DNA A DNA Mapp Seq Anal. 27 (2),
923–924.
Chen, X., Peng, Z., Cai, L., Xu, Y., 2015. Mitochondrial genome of the spot-tail shark
Carcharhinus sorrah (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. 26
(5), 734–735.
Chen, X., Lin, L., Chen, H., Xiang, D., Ai, W., 2016. Complete mitochondrial genome of
the Indonesian whaler shark Carcharhinus tjutjot. Mitochondrial DNA A DNA Mapp
Seq Anal. 27, 3962–3963.
Chen, X., Yu, J., Zhang, S., Ding, W., Xiang, D., 2014. Complete mitochondrial genome of
the tiger shark Galeocerdo cuvier (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA. 25 (6), 441–442.
Li, C., Corrigan, S., Yang, L., Straube, N., Harris, M., Hofreiter, M., White, W.T.,
Naylor, G.J.P., 2015. DNA capture reveals transoceanic gene ow in endangered
river sharks. Proc. Natl. Acad. Sci. USA 112 (43), 13302–13307.
Feutry, P., Grewe, P.M., Kyne, P.M., Chen, X., 2015. Complete mitogenomic sequence of
the Critically Endangered Northern River Shark Glyphis garricki (Carcharhiniformes:
Carcharhinidae). Mitochondrial DNA. 26 (6), 855–856.
Chen, X., Liu, M., Grewe, P.M., Kyne, P.M., Feutry, P., 2014. Complete mitochondrial
genome of the Critically Endangered speartooth shark Glyphis glyphis
(Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. 25 (6), 431–432.
Chen, X., Xiang, D., Ai, W., Shi, X., 2015. Complete mitochondrial genome of the blue
shark Prionace glauca (Elasmobranchii: Carcharhiniformes). Mitochondrial DNA. 26
(2), 313–314.
Liu, Y., Shan, B., Yang, C., Zhao, Y., Liu, M., Xie, Q., Sun, D., 2020. The complete
mitochondrial genome of milk shark, Rhizoprionodon acutus (Ruppell 1837).
Mitochondrial DNA B Resour. 5 (1), 310–311.
C. Wang et al.
Gene 820 (2022) 146232
11
Periasamy, R., Chen, X., Ingole, B., Liu, W., 2016. Complete mitochondrial genome of the
Spadenose shark Scoliodon laticaudus (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA A DNA Mapp Seq Anal. 27 (5), 3248–3249.
Chen, X., Peng, X., Zhang, P., Yang, S., Liu, M., 2014. Complete mitochondrial genome of
the spadenose shark (Scoliodon macrorhynchos). Mitochondrial DNA. 25 (2), 91–92.
Chen, X., Sonchaeng, P., Yuvanatemiya, V., Nuangsaeng, B., Ai, W., 2016. Complete
mitochondrial genome of the whitetip reef shark Triaenodon obesus
(Carcharhiniformes: Carcharhinidae). Mitochondrial DNA A DNA Mapp Seq Anal.
27, 947–948.
Chen, H., Yu, J., Si, R., Chen, X., Ai, W., 2016. Complete mitochondrial genome and the
phylogenetic position of the graceful catshark Proscyllium habereri
(Carcharhiniformes: Proscylliidae). Mitochondrial DNA B Resour. 1 (1), 268–269.
Tanaka, K., Shiina, T., Tomita, T., Suzuki, S., Hosomichi, K., Sano, K., Doi, H., Kono, A.,
Komiyama, T., Inoko, H., Kulski, J.K., Tanaka, S., 2013. Evolutionary relations of
Hexanchiformes deep-sea sharks elucidated by whole mitochondrial genome
sequences. Biomed. Res. Int. 2013, 1–11.
Chen, H., Lin, L., Chen, X., Ai, W., Chen, S., 2016. Complete mitochondrial genome and
the phylogenetic position of the Blotchy swell shark Cephaloscyllium umbratile.
Mitochondrial DNA A DNA Mapp Seq Anal. 27, 3045–3047.
Chen, H., Ding, W., Shan, L., Chen, X., Ai, W., 2016. Complete mitochondrial genome
and the phylogenetic position of the blackspotted catshark Halaelurus burgeri
(Carcharhiniformes: Scyliorhinidae). Mitochondrial DNA B Resour. 1 (1), 369–370.
Delarbre C, Spruyt N, Delmarre C, Gallut C, Barriel V, Janvier P, Laudet V, G. G., The
complete nucleotide sequence of the mitochondrial DNA of the dogsh, Scyliorhinus
canicula, Genetics. 150 (1998) 331–344.
Chen, X., Xiang, D., Xu, Y., Shi, X., 2015. Complete mitochondrial genome of the
scalloped hammerhead Sphyrna lewini (Carcharhiniformes: Sphyrnidae).
Mitochondrial DNA. 26 (4), 621–622.
Ruck, C.L., Marra, N., Shivji, M.S., Stanhope, M.J., 2017. The complete mitochondrial
genome of the endangered great hammerhead shark. Sphyrna mokarran,
Mitochondrial DNA B Resour. 2 (1), 246–248.
Díaz-Jaimes, P., Bayona-V´
asquez, N.J., Adams, D.H., Uribe-Alcocer, M., 2016. Complete
mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic
relationships among main superorders of modern elasmobranchs. Meta. Gene. 7,
48–55.
Bolano-Martinez, N., Bayona-Vasquez, N., Uribe-Alcocer, M., Diaz-Jaimes, P., 2016. The
mitochondrial genome of the hammerhead Sphyrna zygaena. Mitochondrial DNA A
DNA Mapp Seq Anal. 27, 2098–2099.
C. Wang et al.
