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Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae)

Authors:
Jumin Jun at National Institute of Biological Resources
Jumin Jun
Seong-Ho Choi
Seong-Ho Choi
Seong-Ho Choi
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Ji-Don Kum
Ji-Don Kum
Ji-Don Kum
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Abstract

The complete mitochondrial genome of Odontobutis interrupta (Perciformes, Odontobutidae), a species endemic to South Korea, is reported here for the first time. The O. interrupta mitogenome is 16 802 base pairs in total length and includes 13 PCGs, small and large rRNAs, a control region and 22 tRNAs. Nine genes are encoded on the light strand and 29 on the heavy strand. The O. interrupta mitochondrial genome has a conserved gene order compared to four other Odontobutis species and Micropercops swinhonis, a closely related species. The data will provide useful molecular information for phylogenetic studies concerning Odontobutidae and its related species.
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ISSN: 1940-1736 (print), 1940-1744 (electronic)
Mitochondrial DNA, Early Online: 1–3
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2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1060459
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the endemic South Korean species
Odontobutis interrupta (Perciformes, Odontobutidae)
Jumin Jun
1,2
, Seong-Ho Choi
3
, and Ji-Don Kum
4
1
Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea,
2
Division of EcoScience, Ewha Womans
University, Seoul, Republic of Korea,
3
Korean Association for Conservation of Freshwater Fish, Seoul, Republic of Korea, and
4
Natural Live Plankton,
Kyoungsangnam-Do, Republic of Korea
Abstract
The complete mitochondrial genome of Odontobutis interrupta (Perciformes, Odontobutidae),
a species endemic to South Korea, is reported here for the first time. The O. interrupta
mitogenome is 16 802 base pairs in total length and includes 13 PCGs, small and large rRNAs, a
control region and 22 tRNAs. Nine genes are encoded on the light strand and 29 on the heavy
strand. The O. interrupta mitochondrial genome has a conserved gene order compared to four
other Odontobutis species and Micropercops swinhonis, a closely related species. The data will
provide useful molecular information for phylogenetic studies concerning Odontobutidae and
its related species.
Keywords
Endemic species, mitochondrial genome,
Odontobutidae, Odontobutis interrupta,
Perciformes
History
Received 11 May 2015
Accepted 6 June 2015
Published online 30 June 2015
The genus Odontobutis has a limited distribution in far-east Asia
and comprises eight species (Chae, 1999; Chen et al., 2002; Iwata
& Sakai, 2002; Kottelat, 2013). Odontobutis interrupta is
endemic to South Korea and is found mainly in rivers and
tributaries flowing to the western coast of South Korea (Chae,
1999; Jeon & Kim, 1996). Due to its distribution, O. interrupta
is of interest for evolution of the genus; however, genetic
information on the species is lacking.
A specimen of O. interrupta was collected from the
Mangyoung River in Jeollabuk-Do, South Korea. The mitochon-
drial genome was amplified using long-range PCR with two
primer sets used in a previous study (Ki et al., 2008). Then, a
489-bp sequence was obtained using a primer set designed in this
study. The total length of the complete mtDNA is 16 802 bp. The
mitogenome contains large and small rRNAs and 22 tRNA,
a control region and 13 PCGs. Most of the genes are encoded on
the heavy strand, except for ND6 and eight tRNA genes (tRNA
Gln
,
tRNA
Ala
, tRNA
Asn
, tRNA
Cys
, tRNA
Tyr
, tRNA
Ser
, tRNA
Glu
and
tRNA
Pro
).
The overall base composition of the mtDNA is 29.9% A,
29.0% C, 25.5% T and 15.7% G. All of the protein-coding gene
sequences contain the orthodox ATG start codon, except for one
gene, COI, which has GTG as the start codon. Three genes (ND1,
ND3 and ND4) end in the TAG termination codon and eight genes
(ND2, COI, ATP8, ATP6, COIII, ND4L, ND5 and ND6) contain
TAA as the stop codon. The COII gene ends in an AGA
termination codon, while the CYTB gene possesses an incomplete
stop codon and has a terminal T. The lengths of the tRNA gene
sequences vary from 66 bp to 81 bp. Most of the tRNA genes can
be folded into a typical cloverleaf secondary structure. The
mtDNA gene arrangement of O. interrupta is identical to that of
the mitochondrial genomes of four other Odontobutis species
(O. platycephala, O. potamophila, O. yaluensis and O. sinensis)
and Micropercops swinhonis, within the same family (Ki et al.,
2008; Ma et al., 2015a,b,c; Zang et al., 2014). In addition, except
for the positions of three tRNAs (tRNA
Ser
, tRNA
Leu
and tRNA
His
),
the gene arrangement of O. interrupta is identical to the
mitochondrial genome of Perccottus glenii (Chen et al., 2014)
in the same family. Conserved sequence blocks (CSB1 and CSB2)
and three highly conserved areas (C, D and F boxes) were
detected within control region.
The complete mitochondrial genomes of 35 closely related
taxa available in GenBank have been used to reconstruct the NJ
phylogenetic tree (Figure 1). The phylogenetic analyses were
performed using MEGA 6.0 (iGEM, Philadelphia, PA) (Tamura
et al., 2013). Compared with genus Perccottus and Micropercops,
genus Odontobutis is more recently differentiated within family
Odontobutidae. In addition, the phylogenetic tree present that O.
interrupta and O. potamophila are recently differentiated than
other Odontobutis species. Our data will be useful for further
phylogenetic studies of the Odontobutidae and related taxa.
Nucleotide sequence accession number: The complete mito-
chondrial genome sequence of O. interrupta has been assigned the
GenBank accession number KR364945.
Correspondence: Jumin Jun, Animal Resources Division, National
Institute of Biological Resources, 42 Hwankyuong-Ro, Seo-Gu,
Incheon, Republic of Korea. Tel: +82 32 590 7329. Fax: +82 32 590
7250. E-mail: jjm0622@korea.kr
Mitochondrial DNA Downloaded from informahealthcare.com by National Institute of Biological on 06/30/15
For personal use only.
Declaration of interest
This work was funded by the National Institute of Biological Resources of
South Korea, grant number NIBR201514102. The authors report no
conflicts of interest. The authors alone are responsible for the content and
writing of this report.
References
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Figure 1. The neighbor-joining tree of Odontobutis interrupta and related species based on mitochondrial 13 protein-coding gene sequences.
Numbers under branches are bootstrap values by 1000 replicates. The Genbank accession numbers of the sequences are indicated in parentheses after
species name.
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For personal use only.
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... Previous studies on phylogenetic relationships among the Odontobutis species were mostly based on mitochondrial sequences and only involved a few species (Hou et al., 2014;Jun et al., 2016;Lv et al., 2020;Ren and Zhang, 2007;Zang et al., 2016;Zhong et al., 2018). Thus, the phylogenetic relationships of this genus are largely unresolved and inconsistent among different studies. ...
... Odontobutis potamophilus, O. haifengensis, O. interruptus, O. platycephala, O. yaluensis, O. hikimius and O. sinensis were added to this genus subsequently based on morphological characters. Molecular evidences supporting these revisions were few, such as mitochondrial sequence data with scattered taxon sampling (3-5 species) (Hou et al., 2014;Jun et al., 2016;Lv et Due to high similarity in morphological characters, the taxonomic relationship of the genus is still controversal. Odontobutis sinensis had been regarded as O. obscurus in previous studies until Wu et al. (2002) described it as a new species according to morphological evidence. ...
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... Similarly, molecular analyses on the odontobutids are scarce. Mostly only mitochondrial loci and a few taxa were sampled, and the conclusions are inconsistent among studies (Akihito et al., 2000;Jun et al., 2016;Thacker, 2009;Thacker et al., 2015;Zang et al., 2016). The monophyly of the Odontobutidae is generally supported by molecular data, but they often only involved two or three odontobutids and phylogenetic interrelationships within the Odontobutidae are still contentious. ...
... The monophyly of the Odontobutidae is generally supported by molecular data, but they often only involved two or three odontobutids and phylogenetic interrelationships within the Odontobutidae are still contentious. For example, molecular phylogeny based on four mtDNA genes showed that Odontobutis and Perccottus were closely related to each other (Thacker and Hardman, 2005), but in mitochondrial genome analyses, Micropercops and Perccottus were grouped together (Jun et al., 2016;Zang et al., 2016). ...
... Perccottus and the Micropercops were grouped together based on vertebral number and arrangement and having seven to nine first dorsal fin pterygiophores (Birdsong et al., 1988). The sister-taxon relationship between Perccottus and Micropercops was also found in mitochondrial genome analyses (Jun et al., 2016;Zang et al., 2016), but a different study using the same mitochondrial protein coding genes supported Perccottus and Odontobutis as sister group instead of with Micropercops (Ma et al., 2015). ...
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... The 13 mitochondrial protein coding genes and 12S and 16S genes of the samples were extracted to reconstruct a phylogenetic tree. [14][15][16][17][18][19][20]. The respective gene sequences from the above-mentioned species along with M. chalmersi were saved into one fasta file for each gene. ...
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Full-text available
  • Feb 2002
The freshwater goby, Odontobutis hikimius n. sp., is described based on specimens collected from Shimane Prefecture, Japan. The species is unique among Odontobutis in having a connection between the transverse and longitudinal sensory papillae rows on the opercle. It is also distinguishable from congeners by the following combination of characteristics: only a short sensory canal present posterodorsally to eye, lateral scale rows 38–49. Diagnosis of the genus Odontobutis is revised and a key to the seven known species is provided.
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New complete mitochondrial genome of the Perccottus glenii (Perciformes, Odontobutidae): additional non-coding region
Article
  • Mar 2016
  • MITOCHONDR DNA
Abstract Perccottus glenii is a species of freshwater sleeper native to the Russian Far East, north-eastern China, and the northern part of the Korean Penninsula with introduced populations in other regions of Eurasia. In this study, a new complete mitochondrial genome of Perccottus glenii was reported. The circular genome is 16,510 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. Except the origin of the light strand replication (OL), an additional non-coding region was present between ND6 and tRNA-Glu in the Light strand. The overall nucleotide composition was 30.5% A, 29.2% T, 24.4% C and 15.9% G, with an A + T bias of 59.7%. The gene composition and the structural arrangement of the P. glenii complete mtDNA were identical to most of the other vertebrates. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of Odontobutidae fish.
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Complete mitochondrial genome and phylogenic analysis of Odontobutis yaluensis , Perciformes, Odontobutidae
Article
  • Oct 2014
  • MITOCHONDR DNA
Abstract The complete mitochondrial genome of Odontobutis yaluensis was sequenced as to be 16,909 bp in length with (A + T) content of 55.73%, and it contained 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. The gene order and orientation are similar to some typical fish species. The data will provide the useful molecular information for phylogenetic relationships of O. yaluensis with Odontobutis potamophila first clustered into a small branch, and then with Odontobutis platycephala clade, and finally with Odontobutis sinensis clade. Odontobutidae and Rhyacichthyidae formed the sister group, and Eleotridae and Gobiidae formed the sister group.
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Organization of the mitochondrial genome of Odontobutis sinensis (Perciformes: Odontobutidae): Rearrangement of tRNAs and additional non-coding regions
Article
  • Sep 2013
  • MITOCHONDR DNA
Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Odontobutis sinensis. The genome was found to be 17,441 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes) and two main non-coding regions (the control region and the origin of the light strand replication). Rearrangements of tRNAs (tRNA-Ser, tRNA-Leu, tRNA-His) and three additional longer non-coding regions (51 bp, 622 bp and 66 bp, respectively) were present between the ND4 and ND5 genes. Within the control region, one 322 bp long tandem repeat area (7*46 bp) and some typical conserved domains were identified. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of the Odontobutidae.
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Complete mitochondrial genome of the freshwater goby Odontobutis potamophila (Perciformes: Odontobutidae)
Article
  • Sep 2013
  • MITOCHONDR DNA
Abstract In this study, we cloned and sequenced the complete mitochondrial genome of Odontobutis potamophila. The genome was found to be 16,932 bp in size with a mostly conserved structural organization when compared with that of other teleost fish. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and 2 main non-coding regions (the control region and the origin of the light strand replication). Rearrangements of tRNAs (tRNA-Ser, tRNA-Leu, tRNA-His) and three additional longer non-coding regions (43 bp, 336 bp and 76 bp, respectively) were present between the ND4 and ND5 genes. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. This mitogenome sequence data would contribute to better understanding population genetics and phylogenetic analysis of the Odontobutidae.
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The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae)
Article
  • Jul 2013
  • MITOCHONDR DNA
Abstract For understanding the phylogenetic position of Micropercops swinhonis within the family Odontobutidae, the complete nucleotide sequence of M. swinhonis mitochondrial genome was firstly determined. The genome is 16,493 bp in length, and consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and 2 main noncoding regions (the control region and the origin of the light strand replication). The gene composition and order of which were similar to most other vertebrates. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified.
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