http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1018224
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) Xiaoyun Sui1,2, Yangyang Liang2,3, and Dekui He2 School of Life Sciences, Peking University, Beijing, P.R. China, 2Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P.R. China, and 3University of Chinese Academy of Sciences, Beijing, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
1
Abstract
Keywords
The Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) is an ecological important fish in East Asia. In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus. The mitogenome is 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (origin of light– strand replication and control region). The gene content and order is in accord with the common vertebrate form. The nucleotide base composition of H-strand is 28.4% A, 27.2% T, 26.4% C and 18.0% G. The complete mitochondrial genome data would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus.
Chinese minnow, cold water fish, mitochondrial genome, Rhynchocypris oxycephalus
The Rhynchocypris minnows are typical small cold water fish, mainly distributed in Asia (Bogutskaya et al., 2008; Chen, 1998; Jang et al., 2002). The Rhynchocypris oxycephalus (Sauvage et Dabry, 1874) is widely distributed in East Asia, and in China, it is mainly distributed in Yangtze River Basin (Chen, 1998; Zhang & Chen, 1997), at the southern-distribution boundary of Rhynchocypris minnows. As the dominant species, R. oxycephalus plays a crucial role in maintaining the ecological balance of local stream. However, affected by human disturbance and global
History Received 16 January 2015 Accepted 24 January 2015 Published online 23 March 2015
climate change, the population of R. oxycephalus is declining in recent years (Liang et al., 2014; Yu et al., 2013). In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus (Genbank Accession number: KP641342), which would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus. The sample was collected from Laohegou Stream, an upper tributary of the Yangtze River, in Pingwu County, Sichuan Province. Based on the conserved sequences of Phoxinus tumensis
Table 1. Characteristics of the mitochondrial genome of R. oxycephalus. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr
From 1 70 1027 1099 2788 2865 3844 3914 3986 4055 5100 5172 5242 5315 5348 5417
Codon To 69 1026 1098 2787 2863 3839 3915 3984 4054 5101 5170 5240 5314 5347 5415 5487
Size (bp) 69 957 72 1689 76 975 72 71 69 1047 71 69 73 33 68 71
Start
Stop
Amino acid
ATG
TAA
324
ATG
TAG
348
Intergentic nucleotide 0 0 0 0 1 4 2 1 0 2 1 1 0 0 1 1
Strand H H H H H H H L H H H L L – L L (continued )
Correspondence: Dekui He, Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province 430072, P.R. China. Tel: +86 27 68780808. E-mail: [email protected]
2
X. Sui et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
Position
Codon
Locus
From
To
Size (bp)
Start
Stop
Amino acid
Intergentic nucleotide
Strand
COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
5489 7040 7114 7201 7892 7969 8127 8810 9594 9665 10,014 10,083 10,373 11,755 11,824 11,893 11,966 13,798 14,320 14,391 15,532 15,603 15,673
7039 7110 7187 7891 7967 8133 8810 9594 9664 10,015 10,082 10,379 11,755 11,823 11,892 11,965 13,801 14,319 14,388 15,531 15,603 15,672 16,606
1551 71 74 691 76 165 684 785 71 351 69 297 1383 69 69 73 1836 522 69 1141 72 70 934
GTG
TAA
516
ATG
T– –
230
ATG ATG ATG
TAG TAA TA–
54 227 261
ATG
TAG
116
ATG ATG
TAA TAA
98 460
ATG ATG
TAA TAA
611 173
ATG
T– –
380
0 3 13 0 1 7 1 1 0 2 0 7 1 0 0 0 4 0 2 0 1 0
H L H H H H H H H H H H H H H H H L L H H L –
T– – and T– represents incomplete stop codons. The numbers in the intergenic nucleotide column correspond on the nucleotides separating adjacent genes, negative numbers indicate overlapping nucleotides. H and L represent heavy and light strands, respectively.
and Phoxinus phoxinus (Imoto et al., 2013; Xu et al., 2014), we designed 16 pairs of primers for polymerase chain reaction (PCR) amplification. The PCR fragments were assembled by Bioedit software (Hall, 1998) and then calculated the nucleotide base composition by MEGA6.0 (Tamura et al., 2013). To avoid assembling error, the complete mitochondrial sequence was aligned with its closely related species by BLAST. The complete mitogenome of R. oxycephalus was 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two noncoding regions: origin of light–strand replication (OL) and control region (D-loop; Table 1). The gene content and order was in accord with the common vertebrate form (Miya et al., 2001). The 13 protein-coding genes, ranging from 165 to 1836 bp, accounting for the main part (68.8%) of mitogenome. The 22 tRNA genes, ranging from 68 to 76 bp, were interspersed among the mitogenome. The 12S and 16S ribosomal RNA genes, 957 and 1689 bp respectively, were located between tRNAPhe and tRNALeu. All protein-coding genes begin with the representative start codon ATG, with one exception of COXI which began with GTG. Five protein-coding genes share the end codon TAA, five ended with TAG, and the rest protein-coding genes ended with incomplete stop codon T and TA (Table 1). Except for one protein–coding gene (ND6) and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, and tRNAPro) encoded on light-strand (L-strand), most genes were encoded on heavy strand (H–strand). A total of 10 overlaps (ranging from 1 to 7 bp) were detected in R. oxycephalus mitogenome, four overlaps exist among the 13 protein–coding genes (ATP8–ATP6, ATP6–COXIII, ND4L–ND4, and ND5–ND6), two among the 22 tRNA genes (tRNAIle–tRNAGln, tRNAThr– tRNAPro), and four in the pairs of genes ND2–tRNATrp, COXIII– tRNAGly, ND3–tRNAArg, and ND4–tRNAHis. The nucleotide base composition of H-strand was 28.4% A, 27.2% T, 26.4% C and 18.0% G, showing the commonly anti-G bias and slight high A + T content (55.6%).
Acknowledgements The authors thank Mr. Peng Zhao, Mr. Xinggui Cai, and Mr. Xianghui Chen for their help in sample collecting.
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 International Cooperation Program of Chinese Academy of Sciences (No. CN/BEIJING/IHB062113) and National Natural Science Foundation of China (No. 41030208).
References Bogutskaya NG, Naseka AM, Shedko SV, Vasil’eva ED, Chereshnev IA. (2008). The fishes of the Amur River: Updated check-list and zoogeography. Ichthyol Explor Fres 19:301–66. Chen YY. (1998). Fauna Sinica, Osteichthyes, Cypriniformes. Middle Volume. Beijing: Science Press (in Chinese). Hall TA. (1998). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8. Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, et al. (2013). Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514: 112–24. Jang MH, Kim JG, Park SB, Jeong KS, Cho GI, Joo GJ. (2002). The current status of the distribution of introduced fish in large river systems of South Korea. Internat Rev Hydrobiol 87: 319–28. Liang Y, Sui X, Chen Y, Jia Y, He D. (2014). Life history traits of the Chinese minnow Rhynchocypris oxycephalus in the upper branch of Yangtze River, China. Zool Stud. [Epub ahead of print]. DOI: 10.1186/ s40555-014-0036-0. Miya M, Kawaguchi A, Nishida M. (2001). Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined
DOI: 10.3109/19401736.2015.1018224
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
complete mitochondrial DNA sequences. Mol Biol Evol 18: 1993–2009. 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. Xu W, Chen A, Xia R, Fu C. (2014). Complete mitochondrial genome of Phoxinus tumensis (Cypriniformes: Cyprinidae). Mitochondrial DNA 25:368–9.
Mitogenome of R. oxycephalus
3
Yu D, Chen M, Zhou Z, Eric R, Tang Q, Liu H. (2013). Global climate change will severely decrease potential distribution of the East Asian coldwater fish Rhynchocypris oxycephalus (Actinopterygii, Cyprinidae). Hydrobiologia 700:23–32. Zhang E, Chen Y. (1997). Fish fauna in northeastern Jiangxi province with a discussion on the zoogeographical division of east China. Acta Hydrobiol Sin 21:254–61 (in Chinese with English abstract).
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) Xiaoyun Sui1,2, Yangyang Liang2,3, and Dekui He2 School of Life Sciences, Peking University, Beijing, P.R. China, 2Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P.R. China, and 3University of Chinese Academy of Sciences, Beijing, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
1
Abstract
Keywords
The Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) is an ecological important fish in East Asia. In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus. The mitogenome is 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (origin of light– strand replication and control region). The gene content and order is in accord with the common vertebrate form. The nucleotide base composition of H-strand is 28.4% A, 27.2% T, 26.4% C and 18.0% G. The complete mitochondrial genome data would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus.
Chinese minnow, cold water fish, mitochondrial genome, Rhynchocypris oxycephalus
The Rhynchocypris minnows are typical small cold water fish, mainly distributed in Asia (Bogutskaya et al., 2008; Chen, 1998; Jang et al., 2002). The Rhynchocypris oxycephalus (Sauvage et Dabry, 1874) is widely distributed in East Asia, and in China, it is mainly distributed in Yangtze River Basin (Chen, 1998; Zhang & Chen, 1997), at the southern-distribution boundary of Rhynchocypris minnows. As the dominant species, R. oxycephalus plays a crucial role in maintaining the ecological balance of local stream. However, affected by human disturbance and global
History Received 16 January 2015 Accepted 24 January 2015 Published online 23 March 2015
climate change, the population of R. oxycephalus is declining in recent years (Liang et al., 2014; Yu et al., 2013). In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus (Genbank Accession number: KP641342), which would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus. The sample was collected from Laohegou Stream, an upper tributary of the Yangtze River, in Pingwu County, Sichuan Province. Based on the conserved sequences of Phoxinus tumensis
Table 1. Characteristics of the mitochondrial genome of R. oxycephalus. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr
From 1 70 1027 1099 2788 2865 3844 3914 3986 4055 5100 5172 5242 5315 5348 5417
Codon To 69 1026 1098 2787 2863 3839 3915 3984 4054 5101 5170 5240 5314 5347 5415 5487
Size (bp) 69 957 72 1689 76 975 72 71 69 1047 71 69 73 33 68 71
Start
Stop
Amino acid
ATG
TAA
324
ATG
TAG
348
Intergentic nucleotide 0 0 0 0 1 4 2 1 0 2 1 1 0 0 1 1
Strand H H H H H H H L H H H L L – L L (continued )
Correspondence: Dekui He, Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province 430072, P.R. China. Tel: +86 27 68780808. E-mail: [email protected]
2
X. Sui et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
Position
Codon
Locus
From
To
Size (bp)
Start
Stop
Amino acid
Intergentic nucleotide
Strand
COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
5489 7040 7114 7201 7892 7969 8127 8810 9594 9665 10,014 10,083 10,373 11,755 11,824 11,893 11,966 13,798 14,320 14,391 15,532 15,603 15,673
7039 7110 7187 7891 7967 8133 8810 9594 9664 10,015 10,082 10,379 11,755 11,823 11,892 11,965 13,801 14,319 14,388 15,531 15,603 15,672 16,606
1551 71 74 691 76 165 684 785 71 351 69 297 1383 69 69 73 1836 522 69 1141 72 70 934
GTG
TAA
516
ATG
T– –
230
ATG ATG ATG
TAG TAA TA–
54 227 261
ATG
TAG
116
ATG ATG
TAA TAA
98 460
ATG ATG
TAA TAA
611 173
ATG
T– –
380
0 3 13 0 1 7 1 1 0 2 0 7 1 0 0 0 4 0 2 0 1 0
H L H H H H H H H H H H H H H H H L L H H L –
T– – and T– represents incomplete stop codons. The numbers in the intergenic nucleotide column correspond on the nucleotides separating adjacent genes, negative numbers indicate overlapping nucleotides. H and L represent heavy and light strands, respectively.
and Phoxinus phoxinus (Imoto et al., 2013; Xu et al., 2014), we designed 16 pairs of primers for polymerase chain reaction (PCR) amplification. The PCR fragments were assembled by Bioedit software (Hall, 1998) and then calculated the nucleotide base composition by MEGA6.0 (Tamura et al., 2013). To avoid assembling error, the complete mitochondrial sequence was aligned with its closely related species by BLAST. The complete mitogenome of R. oxycephalus was 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two noncoding regions: origin of light–strand replication (OL) and control region (D-loop; Table 1). The gene content and order was in accord with the common vertebrate form (Miya et al., 2001). The 13 protein-coding genes, ranging from 165 to 1836 bp, accounting for the main part (68.8%) of mitogenome. The 22 tRNA genes, ranging from 68 to 76 bp, were interspersed among the mitogenome. The 12S and 16S ribosomal RNA genes, 957 and 1689 bp respectively, were located between tRNAPhe and tRNALeu. All protein-coding genes begin with the representative start codon ATG, with one exception of COXI which began with GTG. Five protein-coding genes share the end codon TAA, five ended with TAG, and the rest protein-coding genes ended with incomplete stop codon T and TA (Table 1). Except for one protein–coding gene (ND6) and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, and tRNAPro) encoded on light-strand (L-strand), most genes were encoded on heavy strand (H–strand). A total of 10 overlaps (ranging from 1 to 7 bp) were detected in R. oxycephalus mitogenome, four overlaps exist among the 13 protein–coding genes (ATP8–ATP6, ATP6–COXIII, ND4L–ND4, and ND5–ND6), two among the 22 tRNA genes (tRNAIle–tRNAGln, tRNAThr– tRNAPro), and four in the pairs of genes ND2–tRNATrp, COXIII– tRNAGly, ND3–tRNAArg, and ND4–tRNAHis. The nucleotide base composition of H-strand was 28.4% A, 27.2% T, 26.4% C and 18.0% G, showing the commonly anti-G bias and slight high A + T content (55.6%).
Acknowledgements The authors thank Mr. Peng Zhao, Mr. Xinggui Cai, and Mr. Xianghui Chen for their help in sample collecting.
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 International Cooperation Program of Chinese Academy of Sciences (No. CN/BEIJING/IHB062113) and National Natural Science Foundation of China (No. 41030208).
References Bogutskaya NG, Naseka AM, Shedko SV, Vasil’eva ED, Chereshnev IA. (2008). The fishes of the Amur River: Updated check-list and zoogeography. Ichthyol Explor Fres 19:301–66. Chen YY. (1998). Fauna Sinica, Osteichthyes, Cypriniformes. Middle Volume. Beijing: Science Press (in Chinese). Hall TA. (1998). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8. Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, et al. (2013). Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514: 112–24. Jang MH, Kim JG, Park SB, Jeong KS, Cho GI, Joo GJ. (2002). The current status of the distribution of introduced fish in large river systems of South Korea. Internat Rev Hydrobiol 87: 319–28. Liang Y, Sui X, Chen Y, Jia Y, He D. (2014). Life history traits of the Chinese minnow Rhynchocypris oxycephalus in the upper branch of Yangtze River, China. Zool Stud. [Epub ahead of print]. DOI: 10.1186/ s40555-014-0036-0. Miya M, Kawaguchi A, Nishida M. (2001). Mitogenomic exploration of higher teleostean phylogenies: A case study for moderate-scale evolutionary genomics with 38 newly determined
DOI: 10.3109/19401736.2015.1018224
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 04/03/15 For personal use only.
complete mitochondrial DNA sequences. Mol Biol Evol 18: 1993–2009. 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. Xu W, Chen A, Xia R, Fu C. (2014). Complete mitochondrial genome of Phoxinus tumensis (Cypriniformes: Cyprinidae). Mitochondrial DNA 25:368–9.
Mitogenome of R. oxycephalus
3
Yu D, Chen M, Zhou Z, Eric R, Tang Q, Liu H. (2013). Global climate change will severely decrease potential distribution of the East Asian coldwater fish Rhynchocypris oxycephalus (Actinopterygii, Cyprinidae). Hydrobiologia 700:23–32. Zhang E, Chen Y. (1997). Fish fauna in northeastern Jiangxi province with a discussion on the zoogeographical division of east China. Acta Hydrobiol Sin 21:254–61 (in Chinese with English abstract).
