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
Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) Heng Wang, Liping He, Xiaoxue Yang, Chen Li, Jiangwen Gu, Xiarong Wang, Gaopeng Li, Shoubao Yang & Lingyan Cao To cite this article: Heng Wang, Liping He, Xiaoxue Yang, Chen Li, Jiangwen Gu, Xiarong Wang, Gaopeng Li, Shoubao Yang & Lingyan Cao (2014): Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945529
Published online: 04 Aug 2014.
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Date: 05 November 2015, At: 20:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945529
MITOGENOME ANNOUNCEMENT
Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) Heng Wang1*, Liping He1*, Xiaoxue Yang2*, Chen Li1*, Jiangwen Gu1, Xiarong Wang1, Gaopeng Li1, Shoubao Yang1, and Lingyan Cao1 College of Life Sciences, Shaoxing University, Shaoxing, P.R. China and 2College of Life Sciences, Anhui Normal University, Wuhu, P.R. China
Downloaded by [Texas A & M International University] at 20:10 05 November 2015
1
Abstract
Keywords
In the present study, the complete mitochondrial genome of the Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) was sequenced and identified, the phylogenetic analysis with other individual of Sarcocheilichthys fishes was carried out. Totally, this genome is 16,679 bp in length, which consists of 13 PCDs, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The total base composition is: 30.05% A, 26.40% T, 26.70% C, and 16.85% G, respectively. These results will provide useful data for species identification and genetics study of Sarcocheilichthys fishes.
Identification, mitogenome, Sarcocheilichthys nigripinnis
Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae), is a small benthopelagic fish widely distributed in various freshwater system of East Asia, especially in China (Zhang et al., 2008), and it has been used a represent species of freshwater fishes in China in biogeographic analysis (Liu et al., 2013). The complete mitochondrial genome sequence could be useful data for population genetics and conservation biology study of aquatic animals (Tang et al., 2011; Yang et al., 2013). In the present study, the complete mitogenome sequence of S. nigripinnis (designated SN2) was sequenced, which was an individual that collected from Huangshan city, Anhui province, China.
History Received 13 June 2014 Revised 15 June 2014 Accepted 27 June 2014 Published online 4 August 2014
The complete mitogenome of S. nigripinnis (Cypriniformes: Cyprinidae) was determined to be 16,679 bp in size (GenBank accession no. KJ997940). Twelve pairs of specific primers were designed according to the complete mitogenome sequences of S. nigripinnis (Genbank no. NC_020608, designated SN-1; Tang et al., 2013) and other Sarcocheilichthys fishes (Yang et al., 2013). The PCR reaction was carried out using the following parameters: initial denaturation at 94 C for 4 min, followed by 35 cycles of amplification (94 C for 50 s, 52–56 C for 25 s, 72 C for 90 s) and 1 final cycle of 10 min at 72 C.
Table 1. Organization of the mitogenome of S. nigripinni. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL
From 1 70 1030 1102 2793 2870 3849 3919 3991 4060 5106 5180 5250 5323
Codon To 69 1029 1101 2791 2868 3844 3920 3989 4059 5105 5177 5248 5322 5353
Size nucleotide (bp) 69 960 72 1690 76 975 72 71 69 1046 72 69 73 31
Start
Stop
Aminoacid
Anti-codon
Intergenic nucleotide
Strand
GAA
0 0 0 0 1 4 –2 1 0 0 2 1 0 0
H H H H H H H L H H H L L
TAC TAA ATG
TAA
324 GAT TTG CAT
ATG
TA–
348 TCA TGC GTT
(continued )
*These authors contributed equally to this work. Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, P.R. China. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
H. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Locus
Downloaded by [Texas A & M International University] at 20:10 05 November 2015
Cys
tRNA tRNATyr COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Codon
From
To
Size nucleotide (bp)
5354 5423 5495 7046 7120 7200 7891 7968 8126 8809 9593 9665 10,015 10,085 10,375 11,757 11,826 11,896 11,969 13,798 14,320 14,393 15,534 15,606 15,675
5421 5493 7045 7116 7191 7890 7966 8132 8809 9592 9664 10,014 10,084 10,381 11,756 11,825 11,894 11,968 13,801 14,319 14,388 15,533 15,605 15,674 16,679
68 71 1551 71 72 691 76 165 684 784 72 350 70 297 1382 69 69 73 1833 522 69 1141 72 69 1005
Start
GTG
Stop
TAA
Aminoacid
Anti-codon
Intergenic nucleotide
Strand
GCA GTA
1 1 0 3 8 0 1 –7 –1 0 0 0 0 –7 0 0 1 0 –4 0 4 0 0 0
L L H L H H H H H H H H H H H H H H H L L H H L –
516 TGA GTC
ATG
T– –
230
ATG ATG ATG
TAA TAA T– –
54 227 261
ATG
TA–
116
ATG ATG
TAA TA–
98 460
TTT
TCC TCG GTG TAG ATG ATG
TAA TAA
611 173
ATG
T– –
380
TTC
The mitogenome of S. nigripinnis contains of 13 proteincoding genes (PCDs), 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (CR; Table 1). The total organization, gene arrangement pattern of the mitochondrial genome, and other characteristics were identical to the typical mitogenome of vertebrate species (Jondeung & Karinthanyakit, 2010). Except for the NADH dehydrogenase 6 (ND6) and eight tRNA genes including tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro are encoded on the L-strand, all the other mitochondrial genes were encoded on H-strand. Total base composition of the mitogenome sequence of S. nigripinnis was about: 30.05% A, 26.40% T, 26.70% C, and 16.85% G, respectively. COX I initiated with a GTG while all other PCDs started with an ATG. Seven PCDs ended with a complete termination codon – TAA (ND1, COX I, ATP8, ATP6, ND4L, ND5, and ND6), while the remaining three genes ended with incomplete terminate codons, either TA (ND2, ND3, and ND4) or T (COX II, COX III, and Cyt b). Phylogenetic analysis was carried out based on the complete mitochondrial genome sequences of several Sarcocheilichthys fishes including S. nigripinnis (SN-1, GenBank accession no. NC_020608) (Tang et al., 2013), S. nigripinnis (SN-2, GenBank accession no. KJ997940), S. parvus (Genbank no. NC_018786; Chen et al., 2013), S. sinensis sinensis (GenBank accession no. KC847084; Yang et al., 2013), and S. lacustris (GenBank accession no. NC_022934). The results showed that two S. nigripinnis (SN-1 and SN-2) are clustered together, and then with S. parvus. We hope these results will provide useful data for species identification and genetics study of Sarcocheilichthys fishes.
TGT TGG
Acknowledgements This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang Province (2011C22084), and the Student Research Foundation of Shaoxing University.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Chen X, Zhou Z, Chen Z, Ai W. (2013). Complete mitochondrial genome of Sarcocheilichthys parvus (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:97–8. Jondeung A, Karinthanyakit W. (2010). The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47. Liu SQ, Tang QY, Li XJ, Liu HZ. (2013). Phylogeographic analyses of Sarcocheilichthys nigripinnis (Teleostei: Cyprinidae) based on mitochondrial DNA Cyt b gene sequences. Zool Res 34:437 45. Tang KL, Agnew MK, Chen WJ, Vincent Hirt M, Raley ME, Sado T, Schneider LM, et al. (2011). Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103–24. Tang WR, Lin HD, Su LW, Tang WQ, Wu CY, Yang JQ. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys nigripinnis (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:478–80. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI:10.3109/19401736.2013.796461. Zhang L, Tang QY, Liu HZ. (2008). Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys. J Fish Biol 72: 1122–37.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) Heng Wang, Liping He, Xiaoxue Yang, Chen Li, Jiangwen Gu, Xiarong Wang, Gaopeng Li, Shoubao Yang & Lingyan Cao To cite this article: Heng Wang, Liping He, Xiaoxue Yang, Chen Li, Jiangwen Gu, Xiarong Wang, Gaopeng Li, Shoubao Yang & Lingyan Cao (2014): Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945529
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 11
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: [Texas A & M International University]
Date: 05 November 2015, At: 20:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945529
MITOGENOME ANNOUNCEMENT
Identification of the mitogenome of Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) Heng Wang1*, Liping He1*, Xiaoxue Yang2*, Chen Li1*, Jiangwen Gu1, Xiarong Wang1, Gaopeng Li1, Shoubao Yang1, and Lingyan Cao1 College of Life Sciences, Shaoxing University, Shaoxing, P.R. China and 2College of Life Sciences, Anhui Normal University, Wuhu, P.R. China
Downloaded by [Texas A & M International University] at 20:10 05 November 2015
1
Abstract
Keywords
In the present study, the complete mitochondrial genome of the Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae) was sequenced and identified, the phylogenetic analysis with other individual of Sarcocheilichthys fishes was carried out. Totally, this genome is 16,679 bp in length, which consists of 13 PCDs, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. The total base composition is: 30.05% A, 26.40% T, 26.70% C, and 16.85% G, respectively. These results will provide useful data for species identification and genetics study of Sarcocheilichthys fishes.
Identification, mitogenome, Sarcocheilichthys nigripinnis
Sarcocheilichthys nigripinnis (Cypriniformes: Cyprinidae), is a small benthopelagic fish widely distributed in various freshwater system of East Asia, especially in China (Zhang et al., 2008), and it has been used a represent species of freshwater fishes in China in biogeographic analysis (Liu et al., 2013). The complete mitochondrial genome sequence could be useful data for population genetics and conservation biology study of aquatic animals (Tang et al., 2011; Yang et al., 2013). In the present study, the complete mitogenome sequence of S. nigripinnis (designated SN2) was sequenced, which was an individual that collected from Huangshan city, Anhui province, China.
History Received 13 June 2014 Revised 15 June 2014 Accepted 27 June 2014 Published online 4 August 2014
The complete mitogenome of S. nigripinnis (Cypriniformes: Cyprinidae) was determined to be 16,679 bp in size (GenBank accession no. KJ997940). Twelve pairs of specific primers were designed according to the complete mitogenome sequences of S. nigripinnis (Genbank no. NC_020608, designated SN-1; Tang et al., 2013) and other Sarcocheilichthys fishes (Yang et al., 2013). The PCR reaction was carried out using the following parameters: initial denaturation at 94 C for 4 min, followed by 35 cycles of amplification (94 C for 50 s, 52–56 C for 25 s, 72 C for 90 s) and 1 final cycle of 10 min at 72 C.
Table 1. Organization of the mitogenome of S. nigripinni. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL
From 1 70 1030 1102 2793 2870 3849 3919 3991 4060 5106 5180 5250 5323
Codon To 69 1029 1101 2791 2868 3844 3920 3989 4059 5105 5177 5248 5322 5353
Size nucleotide (bp) 69 960 72 1690 76 975 72 71 69 1046 72 69 73 31
Start
Stop
Aminoacid
Anti-codon
Intergenic nucleotide
Strand
GAA
0 0 0 0 1 4 –2 1 0 0 2 1 0 0
H H H H H H H L H H H L L
TAC TAA ATG
TAA
324 GAT TTG CAT
ATG
TA–
348 TCA TGC GTT
(continued )
*These authors contributed equally to this work. Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, P.R. China. Tel/Fax: 86-575-88342955. E-mail: [email protected]
2
H. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Locus
Downloaded by [Texas A & M International University] at 20:10 05 November 2015
Cys
tRNA tRNATyr COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Codon
From
To
Size nucleotide (bp)
5354 5423 5495 7046 7120 7200 7891 7968 8126 8809 9593 9665 10,015 10,085 10,375 11,757 11,826 11,896 11,969 13,798 14,320 14,393 15,534 15,606 15,675
5421 5493 7045 7116 7191 7890 7966 8132 8809 9592 9664 10,014 10,084 10,381 11,756 11,825 11,894 11,968 13,801 14,319 14,388 15,533 15,605 15,674 16,679
68 71 1551 71 72 691 76 165 684 784 72 350 70 297 1382 69 69 73 1833 522 69 1141 72 69 1005
Start
GTG
Stop
TAA
Aminoacid
Anti-codon
Intergenic nucleotide
Strand
GCA GTA
1 1 0 3 8 0 1 –7 –1 0 0 0 0 –7 0 0 1 0 –4 0 4 0 0 0
L L H L H H H H H H H H H H H H H H H L L H H L –
516 TGA GTC
ATG
T– –
230
ATG ATG ATG
TAA TAA T– –
54 227 261
ATG
TA–
116
ATG ATG
TAA TA–
98 460
TTT
TCC TCG GTG TAG ATG ATG
TAA TAA
611 173
ATG
T– –
380
TTC
The mitogenome of S. nigripinnis contains of 13 proteincoding genes (PCDs), 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (CR; Table 1). The total organization, gene arrangement pattern of the mitochondrial genome, and other characteristics were identical to the typical mitogenome of vertebrate species (Jondeung & Karinthanyakit, 2010). Except for the NADH dehydrogenase 6 (ND6) and eight tRNA genes including tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro are encoded on the L-strand, all the other mitochondrial genes were encoded on H-strand. Total base composition of the mitogenome sequence of S. nigripinnis was about: 30.05% A, 26.40% T, 26.70% C, and 16.85% G, respectively. COX I initiated with a GTG while all other PCDs started with an ATG. Seven PCDs ended with a complete termination codon – TAA (ND1, COX I, ATP8, ATP6, ND4L, ND5, and ND6), while the remaining three genes ended with incomplete terminate codons, either TA (ND2, ND3, and ND4) or T (COX II, COX III, and Cyt b). Phylogenetic analysis was carried out based on the complete mitochondrial genome sequences of several Sarcocheilichthys fishes including S. nigripinnis (SN-1, GenBank accession no. NC_020608) (Tang et al., 2013), S. nigripinnis (SN-2, GenBank accession no. KJ997940), S. parvus (Genbank no. NC_018786; Chen et al., 2013), S. sinensis sinensis (GenBank accession no. KC847084; Yang et al., 2013), and S. lacustris (GenBank accession no. NC_022934). The results showed that two S. nigripinnis (SN-1 and SN-2) are clustered together, and then with S. parvus. We hope these results will provide useful data for species identification and genetics study of Sarcocheilichthys fishes.
TGT TGG
Acknowledgements This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang Province (2011C22084), and the Student Research Foundation of Shaoxing University.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Chen X, Zhou Z, Chen Z, Ai W. (2013). Complete mitochondrial genome of Sarcocheilichthys parvus (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:97–8. Jondeung A, Karinthanyakit W. (2010). The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47. Liu SQ, Tang QY, Li XJ, Liu HZ. (2013). Phylogeographic analyses of Sarcocheilichthys nigripinnis (Teleostei: Cyprinidae) based on mitochondrial DNA Cyt b gene sequences. Zool Res 34:437 45. Tang KL, Agnew MK, Chen WJ, Vincent Hirt M, Raley ME, Sado T, Schneider LM, et al. (2011). Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 61:103–24. Tang WR, Lin HD, Su LW, Tang WQ, Wu CY, Yang JQ. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys nigripinnis (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:478–80. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. DOI:10.3109/19401736.2013.796461. Zhang L, Tang QY, Liu HZ. (2008). Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys. J Fish Biol 72: 1122–37.
