http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1033693
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Schizothorax lissolabiatus (Cypriniformes: Cyprinidae) Xingjian Yue, Jinrong Shi, Yuanchao Zou, and Bin Wang
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, P. R. China Abstract
Keywords
Schizothorax lissolabiatus is a widely distributed fish species in Lancang River, Yuanjiang River, Pearl River, Nujiang River in China. The complete mitochondrial genome sequence of S. lissolabiatus from Yuanjiang River (the upper Red River) has been sequenced, which is 16,583 bp in length and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 main non-coding regions: origin of light-strand replication and control region. Except for eight tRNA and ND6 genes, most of the genes are encoded on the heavy strand. The length of mitochondrial genome, the order, composition and anticodons of all genes are exactly similar to that of S. dolichonema. The phylogenetic tree suggested S. prenanti, S. dolichonema and S. lissolabiatus may have closer affinities than other fish of the genus Schizothorax.
Complete mitochondrial genome, cyprinidae, Schizothorax lissolabiatus, Yuanjiang River
Schizothorax lissolabiatus (Schizothoracinae, Cyprinidae, Cypriniformes) is a widely distributed fish species in Nujiang River (upper Salween River), Lancang River (upper Mekong River), Pearl River, Yuanjiang River (the upper Red River), the Tibetan Plateau and adjacent areas in China (Chen & Cao, 2000; Yue et al., 2010; Zheng 1989). Due to overfishing, this species is under severe threat, and separated remaining small population in Yuanjiang River and Nujiang River (Yue et al., 2010). The complete mitogenome sequence of S. lissolabiatus is useful in the studies on taxonomic status, biogeography, molecular systematics, stock evaluation and conservation genetics. Here, we determined the complete mitochondrial DNA sequence of S. lissolabiatus. The S. lissolabiatus sample was collected in Zhangba Reservoir (102.20 E, 23.31 N), Yuanjiang County, Yunnan Province, tributary upstream of Yuanjiang River. The complete mtDNA of S. lissolabiatus is 16,583 bp in length (GenBank Accession No. KP796150) and contains 13 proteincoding genes (ATP6, ATP8, CO1-3, ND1-6 and 4L, cytb), 2 ribosomal RNAs (12SrRNA, 16SrRNA), 22 transfer RNA genes and 2 non-coding regions. The overall nucleotide base composition of H-strand was 29.64% A, 27.18% C, 17.87% G and 25.30% T. Most of the genes were encoded on the heavy strand except eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr,
Correspondence: Xingjian Yue, School of Life Sciences, Neijiang Normal University, Neijiang, P. R. China. Tel: +8608322342055. Fax: +8608322341862. E-mail:[email protected]
History Received 21 February 2015 Revised 15 March 2015 Accepted 22 March 2015 Published online 15 May 2015
tRNASer(UCN), tRNAGlu and tRNAPro) and one protein-coding gene (ND6). The total 27 bp overlapped nucleotides were scattered in 10 pairs of genes, tRNAIle–tRNAGln, tRNAMet–ND2, tRNACys– tRNATyr, ATP8–ATP6, ATP6–COIII, COIII–tRNAGly, ND3– tRNAArg, ND4L–ND4, ND5–ND6, tRNAThr–tRNAPro. Except for COI starting with codon GTG, other protein-coding genes use standard ATG start codon. The termination codons were TAA (ND1, COI, ATP6, COIII, ND4L, ND5, ND6), TAG (ND2, ATP8, ND3) or a single T residue (COII, ND4, cytb). The 12S and 16S rRNA genes were 956 bp and 1677 bp in length, respectively, which were located between tRNAPhe and tRNALeu, and were separated by tRNAVal. The length of 22 tRNA genes ranged from 67 (tRNACys) to 76 bp (tRNALeu(UUR), tRNALys). There were 13 non-coding regions. Control region, the major noncoding region, was 933 bp in length and bound by tRNAPhe and tRNAPro. The second non-coding region, between the tRNAAsn and tRNACys, was 33 bp. The other 11 smaller non-coding intergenic fragments (12 bp) were dispersed throughout the whole genome, totaling 34 bp in length. The length of mitochondrial genome, the order, composition of all genes are exactly similar to that of S. dolichonema (Yue et al., 2014). The phylogenetic relationships within the genus Schizothorax (14 species) (Bao et al., 2014; Chen et al., 2013a,b,c, 2014; Goel et al., 2014a,b,c; Gong et al., 2012; Luan et al., 2014; Sahoo et al., 2013, 2014; Yue et al., 2014; Zhu et al., 2013) were investigated using the completed mitochondrial genomes with outgroup (Cyprinus carpio and Percocypris pingi) (Chang et al., 1994; Li et al., 2013), and examined by the MEGA6 software (Tamura et al., 2013). The maximum-likelihood phylogenetic tree suggested S. prenanti (from upper Dadu River), S. dolichonema (from Yalong River) and S. lissolabiatus to have closer affinities than other fish of the genus Schizothorax. Surprisingly, the phylogenetic analysis placed S. wangchiachii
2
X. Yue et al.
Mitochondrial DNA, Early Online: 1–3
58 Schizothorax progastus KF739399
Figure 1. The maximum likelihood phylogeny tree constructed using Mega 6 with 1000 bootstrap replications, Kimura 2-parameter as a model of nucleotide substitution, and ML heuristic method by gamma distributed with Invariant sites (G + I), resulted from the completed mitochondrial genomes of the genus Schizothorax (14 species) with outgroup (Cyprinus carpio X61010 and Percocypris pingi JX316026).
100
Schizothorax richardsonii KC790369 Schizothorax labiatus KF739398
45
Schizothorax esocinus KF600713 Schizothorax prenanti KJ126773
100
40
100
Schizothorax dolichonema KJ184546 Schizothorax lissolabiatus Schizothorax plagiostomus KF928796
Schizothorax plagiostomus KF928796
100 100
Schizothorax waltoni KC513574
100 Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
77 100
100
Schizothorax oconnori KC513575 Schizothorax wangchiachii KC292197 Schizothorax biddulphi JQ844133 Schizothorax pseudoaksaiensis KM079630
100
Schizothorax pseudoaksaiensis KM243919 Percocypris pingi JX316026 Cyprinus carpio X61010
0.01
(from Jinsha River) in a monophyletic clade, including fishes from Yarlung Tsangpo River (Figure 1).
Declaration of interest The present work was supported by the Science and Technology fund from the Education Department of Sichuan Province, PR China (No.12ZA246) and the science and technology fund from Science, Technology and Intellectual Property Bureau of Neijiang, Sichuan Province, PR China (No.11028). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bao M, Zhang X, Xie C, Wan S, Cai L, Zhou Q. (2014). The complete mitochondrial genome of Schizothorax pseudaksaiensis (Cypriniformes: Cyprinidae), Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.947592. Chen YF, Cao WY. (2000). Schizothoracinae. In: Yue P, editor. Fauna sinica, Osteichthyes, Cypriniformes III (in Chinese). Beijing: Science Press. p. 273–335. Chang YS, Huang FL, Lo TB. (1994). The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138–55. Chen CN, Huang YY, Li H, Long ZH, Lai JS, Liu GX, Zhao G. (2014). The complete mitochondrial genome of Schizothorax prenanti (Tchang) (Teleostei, Cyprinidae, Schizothoracinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.883612. Chen Y, Cheng Q, Qiao H, Chen W, Zhu Y. (2013a). The complete mitochondrial genome structure of Schizothorax oconnori (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:630–2. Chen Y, Cheng Q, Qiao H, Zhu Y, Chen W, Ren G. (2013b). The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:353–5.
Chen Y, Cheng Q, Qiao H, Zhu Y, Chen W. (2013c). The complete mitochondrial genome structure of Schizothorax waltoni (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:642–4. Goel C, Sahoo PK, Barat A. (2014a). Complete mitochondrial genome organization of Schizothorax plagiostomus (Heckel, 1838). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2013.873928. Goel C, Sahoo PK, Barat A. (2014b). Complete mitochondrial genome organization of Schizothorax progastus (McClelland, 1839). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2013.861453. Goel C, Sati J, Barat A, Patiyal RS, Ali S, Sahoo PK. (2014c). Complete mitochondrial genome organization of Schizothorax richardsonii (Gray, 1832). Mitochondrial DNA 25:171–2. Gong XL, Cui ZK, Zhang XY, Wang CH. (2012). Complete mitochondrial DNA sequence of the endangered Tarim schizothoracine (Schizothorax biddulphi Gu¨nther). Mitochondrial DNA 23:385–7. Li YP, Wang JJ, Peng ZG. (2013). The complete mitochondrial genome of Percocypris pingi (Teleostei, Cypriniformes). Mitochondrial DNA 24:40–2. Luan PX, Lu JG, Xue SQ, Zhang XF, Peng LN, Sun XW. (2014). Mitochondrial DNA genome sequence of Ili marinka (Schizothorax pseudoaksaiensis). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.953114. Sahoo PK, Barat A, Bhat FA, Balkhi MH, Goel C. (2013). Complete mitochondrial genome organization of Schizothorax esocinus (Heckel, 1838). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.843084. Sahoo PK, Goel C, Bhat FA, Balkhi MH, Barat A. (2014). Complete mitochondrial genome organization of Schizothorax labiatus (McClelland, 1842). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.861452. 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.
DOI: 10.3109/19401736.2015.1033693
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
Yue X, Wang D, Liu S, Yuan X, Zhang Y, Duan X, Chen D. (2010). Population genetic structure of three schizothoracins in Nujiang River, southwestern China. Acta Ecol Sin 30:6418–29. Yue X, Zhou C, Shi J, Zou Y. (2014). The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.895999.
Complete mitogenome of Schizothorax lissolabiatus
3
Zheng CY. (1989). Fishes of the Zhujiang River. Beijing, China: Science Press. 221–224. Zhu Y, Chen Y, Cheng Q, Qiao H, Chen W. (2013). The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:237–9.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Schizothorax lissolabiatus (Cypriniformes: Cyprinidae) Xingjian Yue, Jinrong Shi, Yuanchao Zou, and Bin Wang
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, P. R. China Abstract
Keywords
Schizothorax lissolabiatus is a widely distributed fish species in Lancang River, Yuanjiang River, Pearl River, Nujiang River in China. The complete mitochondrial genome sequence of S. lissolabiatus from Yuanjiang River (the upper Red River) has been sequenced, which is 16,583 bp in length and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 main non-coding regions: origin of light-strand replication and control region. Except for eight tRNA and ND6 genes, most of the genes are encoded on the heavy strand. The length of mitochondrial genome, the order, composition and anticodons of all genes are exactly similar to that of S. dolichonema. The phylogenetic tree suggested S. prenanti, S. dolichonema and S. lissolabiatus may have closer affinities than other fish of the genus Schizothorax.
Complete mitochondrial genome, cyprinidae, Schizothorax lissolabiatus, Yuanjiang River
Schizothorax lissolabiatus (Schizothoracinae, Cyprinidae, Cypriniformes) is a widely distributed fish species in Nujiang River (upper Salween River), Lancang River (upper Mekong River), Pearl River, Yuanjiang River (the upper Red River), the Tibetan Plateau and adjacent areas in China (Chen & Cao, 2000; Yue et al., 2010; Zheng 1989). Due to overfishing, this species is under severe threat, and separated remaining small population in Yuanjiang River and Nujiang River (Yue et al., 2010). The complete mitogenome sequence of S. lissolabiatus is useful in the studies on taxonomic status, biogeography, molecular systematics, stock evaluation and conservation genetics. Here, we determined the complete mitochondrial DNA sequence of S. lissolabiatus. The S. lissolabiatus sample was collected in Zhangba Reservoir (102.20 E, 23.31 N), Yuanjiang County, Yunnan Province, tributary upstream of Yuanjiang River. The complete mtDNA of S. lissolabiatus is 16,583 bp in length (GenBank Accession No. KP796150) and contains 13 proteincoding genes (ATP6, ATP8, CO1-3, ND1-6 and 4L, cytb), 2 ribosomal RNAs (12SrRNA, 16SrRNA), 22 transfer RNA genes and 2 non-coding regions. The overall nucleotide base composition of H-strand was 29.64% A, 27.18% C, 17.87% G and 25.30% T. Most of the genes were encoded on the heavy strand except eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr,
Correspondence: Xingjian Yue, School of Life Sciences, Neijiang Normal University, Neijiang, P. R. China. Tel: +8608322342055. Fax: +8608322341862. E-mail:[email protected]
History Received 21 February 2015 Revised 15 March 2015 Accepted 22 March 2015 Published online 15 May 2015
tRNASer(UCN), tRNAGlu and tRNAPro) and one protein-coding gene (ND6). The total 27 bp overlapped nucleotides were scattered in 10 pairs of genes, tRNAIle–tRNAGln, tRNAMet–ND2, tRNACys– tRNATyr, ATP8–ATP6, ATP6–COIII, COIII–tRNAGly, ND3– tRNAArg, ND4L–ND4, ND5–ND6, tRNAThr–tRNAPro. Except for COI starting with codon GTG, other protein-coding genes use standard ATG start codon. The termination codons were TAA (ND1, COI, ATP6, COIII, ND4L, ND5, ND6), TAG (ND2, ATP8, ND3) or a single T residue (COII, ND4, cytb). The 12S and 16S rRNA genes were 956 bp and 1677 bp in length, respectively, which were located between tRNAPhe and tRNALeu, and were separated by tRNAVal. The length of 22 tRNA genes ranged from 67 (tRNACys) to 76 bp (tRNALeu(UUR), tRNALys). There were 13 non-coding regions. Control region, the major noncoding region, was 933 bp in length and bound by tRNAPhe and tRNAPro. The second non-coding region, between the tRNAAsn and tRNACys, was 33 bp. The other 11 smaller non-coding intergenic fragments (12 bp) were dispersed throughout the whole genome, totaling 34 bp in length. The length of mitochondrial genome, the order, composition of all genes are exactly similar to that of S. dolichonema (Yue et al., 2014). The phylogenetic relationships within the genus Schizothorax (14 species) (Bao et al., 2014; Chen et al., 2013a,b,c, 2014; Goel et al., 2014a,b,c; Gong et al., 2012; Luan et al., 2014; Sahoo et al., 2013, 2014; Yue et al., 2014; Zhu et al., 2013) were investigated using the completed mitochondrial genomes with outgroup (Cyprinus carpio and Percocypris pingi) (Chang et al., 1994; Li et al., 2013), and examined by the MEGA6 software (Tamura et al., 2013). The maximum-likelihood phylogenetic tree suggested S. prenanti (from upper Dadu River), S. dolichonema (from Yalong River) and S. lissolabiatus to have closer affinities than other fish of the genus Schizothorax. Surprisingly, the phylogenetic analysis placed S. wangchiachii
2
X. Yue et al.
Mitochondrial DNA, Early Online: 1–3
58 Schizothorax progastus KF739399
Figure 1. The maximum likelihood phylogeny tree constructed using Mega 6 with 1000 bootstrap replications, Kimura 2-parameter as a model of nucleotide substitution, and ML heuristic method by gamma distributed with Invariant sites (G + I), resulted from the completed mitochondrial genomes of the genus Schizothorax (14 species) with outgroup (Cyprinus carpio X61010 and Percocypris pingi JX316026).
100
Schizothorax richardsonii KC790369 Schizothorax labiatus KF739398
45
Schizothorax esocinus KF600713 Schizothorax prenanti KJ126773
100
40
100
Schizothorax dolichonema KJ184546 Schizothorax lissolabiatus Schizothorax plagiostomus KF928796
Schizothorax plagiostomus KF928796
100 100
Schizothorax waltoni KC513574
100 Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
77 100
100
Schizothorax oconnori KC513575 Schizothorax wangchiachii KC292197 Schizothorax biddulphi JQ844133 Schizothorax pseudoaksaiensis KM079630
100
Schizothorax pseudoaksaiensis KM243919 Percocypris pingi JX316026 Cyprinus carpio X61010
0.01
(from Jinsha River) in a monophyletic clade, including fishes from Yarlung Tsangpo River (Figure 1).
Declaration of interest The present work was supported by the Science and Technology fund from the Education Department of Sichuan Province, PR China (No.12ZA246) and the science and technology fund from Science, Technology and Intellectual Property Bureau of Neijiang, Sichuan Province, PR China (No.11028). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bao M, Zhang X, Xie C, Wan S, Cai L, Zhou Q. (2014). The complete mitochondrial genome of Schizothorax pseudaksaiensis (Cypriniformes: Cyprinidae), Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.947592. Chen YF, Cao WY. (2000). Schizothoracinae. In: Yue P, editor. Fauna sinica, Osteichthyes, Cypriniformes III (in Chinese). Beijing: Science Press. p. 273–335. Chang YS, Huang FL, Lo TB. (1994). The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138–55. Chen CN, Huang YY, Li H, Long ZH, Lai JS, Liu GX, Zhao G. (2014). The complete mitochondrial genome of Schizothorax prenanti (Tchang) (Teleostei, Cyprinidae, Schizothoracinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.883612. Chen Y, Cheng Q, Qiao H, Chen W, Zhu Y. (2013a). The complete mitochondrial genome structure of Schizothorax oconnori (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:630–2. Chen Y, Cheng Q, Qiao H, Zhu Y, Chen W, Ren G. (2013b). The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:353–5.
Chen Y, Cheng Q, Qiao H, Zhu Y, Chen W. (2013c). The complete mitochondrial genome structure of Schizothorax waltoni (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:642–4. Goel C, Sahoo PK, Barat A. (2014a). Complete mitochondrial genome organization of Schizothorax plagiostomus (Heckel, 1838). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2013.873928. Goel C, Sahoo PK, Barat A. (2014b). Complete mitochondrial genome organization of Schizothorax progastus (McClelland, 1839). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2013.861453. Goel C, Sati J, Barat A, Patiyal RS, Ali S, Sahoo PK. (2014c). Complete mitochondrial genome organization of Schizothorax richardsonii (Gray, 1832). Mitochondrial DNA 25:171–2. Gong XL, Cui ZK, Zhang XY, Wang CH. (2012). Complete mitochondrial DNA sequence of the endangered Tarim schizothoracine (Schizothorax biddulphi Gu¨nther). Mitochondrial DNA 23:385–7. Li YP, Wang JJ, Peng ZG. (2013). The complete mitochondrial genome of Percocypris pingi (Teleostei, Cypriniformes). Mitochondrial DNA 24:40–2. Luan PX, Lu JG, Xue SQ, Zhang XF, Peng LN, Sun XW. (2014). Mitochondrial DNA genome sequence of Ili marinka (Schizothorax pseudoaksaiensis). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.953114. Sahoo PK, Barat A, Bhat FA, Balkhi MH, Goel C. (2013). Complete mitochondrial genome organization of Schizothorax esocinus (Heckel, 1838). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.843084. Sahoo PK, Goel C, Bhat FA, Balkhi MH, Barat A. (2014). Complete mitochondrial genome organization of Schizothorax labiatus (McClelland, 1842). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.861452. 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.
DOI: 10.3109/19401736.2015.1033693
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/16/15 For personal use only.
Yue X, Wang D, Liu S, Yuan X, Zhang Y, Duan X, Chen D. (2010). Population genetic structure of three schizothoracins in Nujiang River, southwestern China. Acta Ecol Sin 30:6418–29. Yue X, Zhou C, Shi J, Zou Y. (2014). The complete mitochondrial genome sequence of Schizothorax dolichonema (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.895999.
Complete mitogenome of Schizothorax lissolabiatus
3
Zheng CY. (1989). Fishes of the Zhujiang River. Beijing, China: Science Press. 221–224. Zhu Y, Chen Y, Cheng Q, Qiao H, Chen W. (2013). The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes: Cyprinidae). Mitochondrial DNA 24:237–9.
