Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae) Jumin Jun, Seong-Ho Choi & Ji-Don Kum To cite this article: Jumin Jun, Seong-Ho Choi & Ji-Don Kum (2015): Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1060459
Published online: 30 Jun 2015.
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Date: 15 September 2015, At: 00:09
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 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 Jun1,2, Seong-Ho Choi3, and Ji-Don Kum4 Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea, 2Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea, 3Korean Association for Conservation of Freshwater Fish, Seoul, Republic of Korea, and 4Natural Live Plankton, Kyoungsangnam-Do, Republic of Korea
Downloaded by [New York University] at 00:09 15 September 2015
1
Abstract
Keywords
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.
Endemic species, mitochondrial genome, Odontobutidae, Odontobutis interrupta, Perciformes
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 mitochondrial 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 (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro). 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,
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: [email protected]
History Received 11 May 2015 Accepted 6 June 2015 Published online 30 June 2015
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 (tRNASer, tRNALeu and tRNAHis), 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 mitochondrial genome sequence of O. interrupta has been assigned the GenBank accession number KR364945.
J. Jun et al.
Mitochondrial DNA, Early Online: 1–3
Downloaded by [New York University] at 00:09 15 September 2015
2
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.
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 Chae BS. (1999). First record of odontobutid fish, Odontobutis obscura (Pisces, Gobioidei) from Korea. Korean J Ichthyol 11: 12–16.
Chen IS, Kottelat M, Wu HL. (2002). A new genus of freshwater sleeper (Teleostei: Odontobutididae) from southern China and mainland southeast Asia. J Fish Soc Taiwan 29:229–35. Chen X, Shi Y, Zhong L, Wang M, Sun L, Yang G. (2014). New complete mitochondrial genome of the Perccottus glenii (Perciformes, Odontobutidae): Additional non-coding region. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.974166. Iwata A, Sakai H. (2002). Odontobutis hikimius n. sp.: A New Freshwater Goby from Japan, with a Key to Species of the Genus. Copeia 2002: 104–10. Jeon SR, Kim YJ. (1996). First record of the Odontobutis interrupta (Gobioidei: Odontobutidae) from Samsan-river and Somjin-river. Korean J Limnol 29:111–17.
DOI: 10.3109/19401736.2015.1060459
Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta
Downloaded by [New York University] at 00:09 15 September 2015
Ki JS, Jung SO, Hwang DS, Lee YM, Lee JS. (2008). Unusual mitochondrial genome structure of the freshwater goby Odontobutis platycephala: Rearrangement of tRNAs and an additional non-coding region. J Fish Biol 73:414–28. Kottelat M. (2013). The fishes of the inland waters of Southeast Asia: A catalogue and core bibliography of the fishes known to occur in freshwater, mangroves and estuaries. Raff Bull Zool 27:1–667. Ma Z, Huang Z, Zhang Z, Xie L, Yang X, Zhang X, Yang R. (2015a). The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae). Mitochondrial DNA 26: 116–17. Ma Z, Yang X, Zhang X, Yang R. (2015b). Complete mitochondrial genome of the freshwater goby Odontobutis
3
potamophila (Perciformes: Odontobutidae). Mitochondrial DNA 26:299–300. Ma Z, Yang X, Zhang X, Yang R, Qiu P. (2015c). Organization of the mitochondrial genome of Odontobutis sinensis (Perciformes: Odontobutidae): Rearrangement of tRNAs and additional non-coding regions. Mitochondrial DNA 26:327–8. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–9. Zang X, Wang X, Zhang G, Wang Y, Ding Y, Yin S. (2014). Complete mitochondrial genome and phylogenic analysis of Odontobutis yaluensis, Perciformes, Odontobutidae. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.971309.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae) Jumin Jun, Seong-Ho Choi & Ji-Don Kum To cite this article: Jumin Jun, Seong-Ho Choi & Ji-Don Kum (2015): Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta (Perciformes, Odontobutidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1060459
Published online: 30 Jun 2015.
Submit your article to this journal
Article views: 5
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [New York University]
Date: 15 September 2015, At: 00:09
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 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 Jun1,2, Seong-Ho Choi3, and Ji-Don Kum4 Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea, 2Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea, 3Korean Association for Conservation of Freshwater Fish, Seoul, Republic of Korea, and 4Natural Live Plankton, Kyoungsangnam-Do, Republic of Korea
Downloaded by [New York University] at 00:09 15 September 2015
1
Abstract
Keywords
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.
Endemic species, mitochondrial genome, Odontobutidae, Odontobutis interrupta, Perciformes
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 mitochondrial 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 (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro). 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,
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: [email protected]
History Received 11 May 2015 Accepted 6 June 2015 Published online 30 June 2015
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 (tRNASer, tRNALeu and tRNAHis), 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 mitochondrial genome sequence of O. interrupta has been assigned the GenBank accession number KR364945.
J. Jun et al.
Mitochondrial DNA, Early Online: 1–3
Downloaded by [New York University] at 00:09 15 September 2015
2
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.
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 Chae BS. (1999). First record of odontobutid fish, Odontobutis obscura (Pisces, Gobioidei) from Korea. Korean J Ichthyol 11: 12–16.
Chen IS, Kottelat M, Wu HL. (2002). A new genus of freshwater sleeper (Teleostei: Odontobutididae) from southern China and mainland southeast Asia. J Fish Soc Taiwan 29:229–35. Chen X, Shi Y, Zhong L, Wang M, Sun L, Yang G. (2014). New complete mitochondrial genome of the Perccottus glenii (Perciformes, Odontobutidae): Additional non-coding region. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.974166. Iwata A, Sakai H. (2002). Odontobutis hikimius n. sp.: A New Freshwater Goby from Japan, with a Key to Species of the Genus. Copeia 2002: 104–10. Jeon SR, Kim YJ. (1996). First record of the Odontobutis interrupta (Gobioidei: Odontobutidae) from Samsan-river and Somjin-river. Korean J Limnol 29:111–17.
DOI: 10.3109/19401736.2015.1060459
Complete mitochondrial genome of the endemic South Korean species Odontobutis interrupta
Downloaded by [New York University] at 00:09 15 September 2015
Ki JS, Jung SO, Hwang DS, Lee YM, Lee JS. (2008). Unusual mitochondrial genome structure of the freshwater goby Odontobutis platycephala: Rearrangement of tRNAs and an additional non-coding region. J Fish Biol 73:414–28. Kottelat M. (2013). The fishes of the inland waters of Southeast Asia: A catalogue and core bibliography of the fishes known to occur in freshwater, mangroves and estuaries. Raff Bull Zool 27:1–667. Ma Z, Huang Z, Zhang Z, Xie L, Yang X, Zhang X, Yang R. (2015a). The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae). Mitochondrial DNA 26: 116–17. Ma Z, Yang X, Zhang X, Yang R. (2015b). Complete mitochondrial genome of the freshwater goby Odontobutis
3
potamophila (Perciformes: Odontobutidae). Mitochondrial DNA 26:299–300. Ma Z, Yang X, Zhang X, Yang R, Qiu P. (2015c). Organization of the mitochondrial genome of Odontobutis sinensis (Perciformes: Odontobutidae): Rearrangement of tRNAs and additional non-coding regions. Mitochondrial DNA 26:327–8. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–9. Zang X, Wang X, Zhang G, Wang Y, Ding Y, Yin S. (2014). Complete mitochondrial genome and phylogenic analysis of Odontobutis yaluensis, Perciformes, Odontobutidae. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.971309.
