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
The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae) Tianheng Gao, Huiwu Tian, Dengqiang Wang, Xinbin Duan, Shaoping Liu & Daqing Chen To cite this article: Tianheng Gao, Huiwu Tian, Dengqiang Wang, Xinbin Duan, Shaoping Liu & Daqing Chen (2015): The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1038796
Published online: 28 May 2015.
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Date: 06 November 2015, At: 00:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1038796
MITOGENOME ANNOUNCEMENT
The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae) Tianheng Gao1,2, Huiwu Tian2, Dengqiang Wang2, Xinbin Duan2, Shaoping Liu2, and Daqing Chen2 1
Downloaded by [NUS National University of Singapore] at 00:44 06 November 2015
Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Science, Southwest University, Chongqing, China and 2Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China Abstract
Keywords
In the present study, the complete mitogenome sequence of Gnathopogon imberbis is determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,598 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The overall nucleotide composition was 30.0% A, 27.0% T, 25.8% C and 17.2% G, with an A + T bias of 57.0%. The complete mitochondrial genome sequence will be useful for phylogenetic analysis and studies of population genetics of G. imberbis.
Cypriniformes, Gnathopogon imberbis, mitogenome
The specimen of Gnathopogon imberbis was collected from Yangtze River, Chongqing, China. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate precipitation protocol (Nicholls et al., 2000). Here we present the complete mitochondrial genome of G. imberbis that was deposited in GenBank with the accession number KR010927. We amplified and sequenced the whole mitochondrial genome sequence of G. imberbis with 14 pairs of primers designed in accordance with equivalent mitochondrial genome sequences of 30 species from Cypriniformes (Wang et al., 2011). All the primers were available upon request. The complete mitochondrial genome of G. imberbis was found to be similar to those of most other vertebrates (Huang et al., 2012). It was sequenced and determined to be 16,598 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. The majority of the mitochondrial genes of G. imberbis are encoded on heavy strand (H-strand) except for ND6 and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu, and Pro), which are encoded on light strand (L-strand).The base composition was analyzed by using MEGA5. The base composition of H-strand was as follows: 30.0% A, 27.0% T, 25.8% C, 17.2% G and AT content was 57.0%. The GC content of Cyprinid mitochondrial genomes is always lower than AT content and this is also an evident in other teleost species (Yue et al., 2006). Mitogenome database was annotated by MitoFish (Iwasaki et al., 2013). Among 13 protein-coding genes, gene overlaps can be observed between three pairs of the contiguous
History Received 26 March 2015 Revised 30 March 2015 Accepted 5 April 2015 Published online 28 May 2015
genes, ATP8-ATP6, ND4L-ND4 and ND5-ND6, and they overlap by seven, seven and four nucleotides, respectively. 64 bp intergenic nucleotides are found in the whole genome, ranging from 1 to 32 bp. As in other bony fishes, all 13 protein-coding genes of G. imberbis share the start codon ATG, except for COI, which begins with GTG. Open reading-frames of four protein-coding genes end with TAA and three proteincoding genes end with TAG, while the others with incomplete stop codons, TA- (ATPase 6) or T- (ND2, COII, COIII, ND3, ND4 and Cyt b). The species, Gnathopogon imberbis is spread in the middle and upper reaches of Yangtze River, China. The complete mitochondrial genomes of G. strigatus, G. elongates and G. polytaenia have been reported in previous studies (Saitoh et al., 2006; Tang et al., 2011; Tao & Zhao, 2014). However, the species of the genus Gnathopogon is rather similar (Naseka, 1996), the molecular systematics for this group of fish remains elusive. In this study, we report the complete mitochondrial genome (mitogenome) of G. imberbis and probably it may play important role in the studies of population genetics and phylogenetic analysis of this species. The phylogenetic tree was reconstructed using neighbor-joining (NJ) method with 1000 bootstrap replicates from 11 members of Gobioninae fishes and G. imberbis (present study) using MEGA 6 (Tamura et al., 2013). As indicated by the trees, fishes of the Gobioninae were divided into four well-defined clades. G. imberbis was closely related to other Gnathopogon fish (Figure 1).
Correspondence: Xinbin Duan, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. E-mail: [email protected]
Downloaded by [NUS National University of Singapore] at 00:44 06 November 2015
2
T. Gao et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Neighbor joining tree reconstructed using Amino: p-distance model with 1000 bootstrap replicates of 12 Gobioninae fish based on the heavy chain protein-coding genes of mitogenome. Scientific name and Genbank accession number of each fish is listed in the tree. Bootstrap values are shown on the nodes in order.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was supported by the project of China Three Gorges Corporation (0799553).
References Huang Y, Zhao G, Peng Z. (2012). Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes). Mitochondrial DNA 23:173–5. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Naseka AM. (1996). Comparative study on the vertebral column in the Gobioninae (cyprinidae, pisces) with special reference to its systematics. Publ Espec Inst Esp Oceanogr 21:149–67. Nicholls JA, Double MC, Rowell DM, Magrath D. (2000). The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). J Avian Biol 31:165–76.
Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–41. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA 6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Tang KL, Agnew MK, Chen W-J, Hirt MV, Raley ME, Sado T, Schneider LM, et al. (2011). Phylogeny of the Gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103–24. Tao W, Zhao H. (2014). The Complete Mitogenome of Gnathopogon Polytaenia (Cypriniformes; Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.945569. Wang J, Li P, Zhang Y, Peng Z. (2011). The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes). Mitochondrial DNA 22:178–80. Yue GH, Liew WC, Orban L. (2006). The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genomics 7:1–13.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae) Tianheng Gao, Huiwu Tian, Dengqiang Wang, Xinbin Duan, Shaoping Liu & Daqing Chen To cite this article: Tianheng Gao, Huiwu Tian, Dengqiang Wang, Xinbin Duan, Shaoping Liu & Daqing Chen (2015): The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1038796
Published online: 28 May 2015.
Submit your article to this journal
Article views: 5
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [NUS National University of Singapore]
Date: 06 November 2015, At: 00:44
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1038796
MITOGENOME ANNOUNCEMENT
The mitochondrial genome of Gnathopogon imberbis (Cypriniformes, Cyprinidae) Tianheng Gao1,2, Huiwu Tian2, Dengqiang Wang2, Xinbin Duan2, Shaoping Liu2, and Daqing Chen2 1
Downloaded by [NUS National University of Singapore] at 00:44 06 November 2015
Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Science, Southwest University, Chongqing, China and 2Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China Abstract
Keywords
In the present study, the complete mitogenome sequence of Gnathopogon imberbis is determined using PCR amplification and DNA sequencing, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,598 bp. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The overall nucleotide composition was 30.0% A, 27.0% T, 25.8% C and 17.2% G, with an A + T bias of 57.0%. The complete mitochondrial genome sequence will be useful for phylogenetic analysis and studies of population genetics of G. imberbis.
Cypriniformes, Gnathopogon imberbis, mitogenome
The specimen of Gnathopogon imberbis was collected from Yangtze River, Chongqing, China. Total genomic DNA from fin tissue was extracted using a modified ammonium acetate precipitation protocol (Nicholls et al., 2000). Here we present the complete mitochondrial genome of G. imberbis that was deposited in GenBank with the accession number KR010927. We amplified and sequenced the whole mitochondrial genome sequence of G. imberbis with 14 pairs of primers designed in accordance with equivalent mitochondrial genome sequences of 30 species from Cypriniformes (Wang et al., 2011). All the primers were available upon request. The complete mitochondrial genome of G. imberbis was found to be similar to those of most other vertebrates (Huang et al., 2012). It was sequenced and determined to be 16,598 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. The majority of the mitochondrial genes of G. imberbis are encoded on heavy strand (H-strand) except for ND6 and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu, and Pro), which are encoded on light strand (L-strand).The base composition was analyzed by using MEGA5. The base composition of H-strand was as follows: 30.0% A, 27.0% T, 25.8% C, 17.2% G and AT content was 57.0%. The GC content of Cyprinid mitochondrial genomes is always lower than AT content and this is also an evident in other teleost species (Yue et al., 2006). Mitogenome database was annotated by MitoFish (Iwasaki et al., 2013). Among 13 protein-coding genes, gene overlaps can be observed between three pairs of the contiguous
History Received 26 March 2015 Revised 30 March 2015 Accepted 5 April 2015 Published online 28 May 2015
genes, ATP8-ATP6, ND4L-ND4 and ND5-ND6, and they overlap by seven, seven and four nucleotides, respectively. 64 bp intergenic nucleotides are found in the whole genome, ranging from 1 to 32 bp. As in other bony fishes, all 13 protein-coding genes of G. imberbis share the start codon ATG, except for COI, which begins with GTG. Open reading-frames of four protein-coding genes end with TAA and three proteincoding genes end with TAG, while the others with incomplete stop codons, TA- (ATPase 6) or T- (ND2, COII, COIII, ND3, ND4 and Cyt b). The species, Gnathopogon imberbis is spread in the middle and upper reaches of Yangtze River, China. The complete mitochondrial genomes of G. strigatus, G. elongates and G. polytaenia have been reported in previous studies (Saitoh et al., 2006; Tang et al., 2011; Tao & Zhao, 2014). However, the species of the genus Gnathopogon is rather similar (Naseka, 1996), the molecular systematics for this group of fish remains elusive. In this study, we report the complete mitochondrial genome (mitogenome) of G. imberbis and probably it may play important role in the studies of population genetics and phylogenetic analysis of this species. The phylogenetic tree was reconstructed using neighbor-joining (NJ) method with 1000 bootstrap replicates from 11 members of Gobioninae fishes and G. imberbis (present study) using MEGA 6 (Tamura et al., 2013). As indicated by the trees, fishes of the Gobioninae were divided into four well-defined clades. G. imberbis was closely related to other Gnathopogon fish (Figure 1).
Correspondence: Xinbin Duan, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. E-mail: [email protected]
Downloaded by [NUS National University of Singapore] at 00:44 06 November 2015
2
T. Gao et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Neighbor joining tree reconstructed using Amino: p-distance model with 1000 bootstrap replicates of 12 Gobioninae fish based on the heavy chain protein-coding genes of mitogenome. Scientific name and Genbank accession number of each fish is listed in the tree. Bootstrap values are shown on the nodes in order.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This study was supported by the project of China Three Gorges Corporation (0799553).
References Huang Y, Zhao G, Peng Z. (2012). Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes). Mitochondrial DNA 23:173–5. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Naseka AM. (1996). Comparative study on the vertebral column in the Gobioninae (cyprinidae, pisces) with special reference to its systematics. Publ Espec Inst Esp Oceanogr 21:149–67. Nicholls JA, Double MC, Rowell DM, Magrath D. (2000). The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae). J Avian Biol 31:165–76.
Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M. (2006). Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–41. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA 6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Tang KL, Agnew MK, Chen W-J, Hirt MV, Raley ME, Sado T, Schneider LM, et al. (2011). Phylogeny of the Gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103–24. Tao W, Zhao H. (2014). The Complete Mitogenome of Gnathopogon Polytaenia (Cypriniformes; Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2014.945569. Wang J, Li P, Zhang Y, Peng Z. (2011). The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes). Mitochondrial DNA 22:178–80. Yue GH, Liew WC, Orban L. (2006). The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genomics 7:1–13.
