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
Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae) Heng Wang, Xiaoxue Yang, Xiarong Wang, Chen Li, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv & Pingping Huang To cite this article: Heng Wang, Xiaoxue Yang, Xiarong Wang, Chen Li, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv & Pingping Huang (2014): Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947596
Published online: 08 Aug 2014.
Submit your article to this journal
Article views: 18
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: [University of Lethbridge]
Date: 05 November 2015, At: 15:32
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947596
MITOGENOME ANNOUNCEMENT
Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae) Heng Wang*, Xiaoxue Yang*, Xiarong Wang*, Chen Li*, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv, and Pingping Huang
Downloaded by [University of Lethbridge] at 15:32 05 November 2015
College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of Abbottina rivularis was determined; the phylogenetic analysis with other individuals and closely related species of the gudgeons was carried out. The complete mitogenome of A. rivularis was 16,597 bp in length, which consists of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 2 non-coding regions: (D-loop and OL). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%). This study provides useful data to genetics, conservation and evolution study of the gudgeons.
Abbottina rivularis, mitogenome, sequencing
Abbottina rivularis (Cypriniformes: Cyprinidae), is a small benthopelagic freshwater species of ray-finned fish in the family Cyprinidae. It is distributed widely in China, and also distributed in Korea and Japan. The mitochondrial genome sequence could provide useful information for genetics, conservation and evolution study of many aquatic species (Wang et al., 2013; Yang et al., 2014). Ten pairs of primers were used in this study, which were designed according to the complete mitochondrial genome sequence of A. rivularis (GenBank accession no. KF577979.1,
History Received 14 July 2014 Accepted 19 July 2014 Published online 8 August 2014
designated Ar-1) (He et al., 2013), which was a different individual of the same species that sampled from different places. PCR amplification was carried out in a total volume of 25 ml, including 60 ng template DNA, 1 U Taq DNA polymerase, 0.2 mM dNTP, 2 mM MgCl2, 20 pM of the sense and anti-sense primer each. The complete mitochondrial genome of A. rivularis (designated Ar-3) was sequenced and determined (16,597 bp in length, GenBank accession no. KM081703), which consists of 22 tRNA genes, 13 protein-coding genes (PCDs), 2 rRNA genes, and
Table 1. Organization of the mitochondrial genome of A. rivularis. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr
Abbreviations F 12S V 16S L nd1 I Q M nd2 W A N C Y
From 1 70 1024 1096 2784 2860 3838 3908 3980 4049 5094 5168 5238 5311 5342 5412
To 69 1023 1095 2783 2859 3834 3909 3978 4048 5093 5165 5236 5310 5341 5410 5482
Codon Size (bp) 69 954 72 1688 76 975 72 71 69 1045 72 69 73 31 69 71
Start
Stop
Amino acid
Anti-codon GAA TAC TAA
ATG
TAA
324 GAT TTG CAT
ATG
T– –
348 TCA TGC GTT GCA GTA
Intergenic nucleotide 0 0 0 0 0 3 2 1 0 0 2 1 0 0 1 1
Strand H H H H H H H L H H H L L L L
(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
Downloaded by [University of Lethbridge] at 15:32 05 November 2015
Locus 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
Abbreviations
From
To
Size (bp)
Start
Stop
Amino acid
cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
5484 7035 7109 7194 7885 7962 8120 8803 9587 9659 10,009 10,079 10,369 11,751 11,820 11,890 11,963 13,795 14,317 14,388 15,529 15,599 15,669
7034 7105 7180 7884 7960 8126 8803 9586 9658 10,008 10,078 10,375 11,750 11,819 11,888 11,962 13,798 14,316 14,385 15,528 15,599 15,668 16,597
1551 71 72 691 76 165 684 784 72 350 70 297 1382 69 69 73 1836 522 69 1141 71 70 929
GTG
TAA
516
Anti-codon 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
2 non-coding regions (Table 1). All of these genes were encoded on the heavy strand (H-strand), with the exception of one PCD (ND6) and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro; Table 1). All of the genes showed typical gene arrangement that similar to the vertebrate species (Jondeung & Karinthanyakit, 2010). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%) as that of other vertebrate mitochondrial genome. Phylogenetic tree was constructed based on the complete mitochondrial genome sequences of A. rivularis (GenBank accession no. KF577979.1, designated Ar-1; He et al., 2013), A. rivularis (GenBank accession no. KM081703, designated Ar-2) (Liu et al., 2014), A. rivularis (GenBank accession no. KM081703, designated Ar-3), Biwia springeri (GenBank accession no. AP011360.1) (Tang et al., 2011), Microphysogobio brevirostris (GenBank accession no. KF319122.1), and Romanogobio tenuicorpus (GenBank accession no. KF647873.1; Dong et al., 2014) using the neighbor-joining method (figure not shown). It showed that A. rivularis (Ar-3) is clustered with Ar-1 and Ar-2. This study provides useful data to genetics, conservation and evolution study of the gudgeons.
Declaration of interest This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang province (2011C22084); Student Innovation Training Program of Shaoxing University (2014). The authors
TGT TGG
Intergenic nucleotide
Strand
0 3 13 0 1 7 1 0 0 0 0 7 0 0 1 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 –
report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Dong F, Tong GX, Kuang YY, Sun XW. (2014). Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur white fin gudgeon). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.865169. He H, Wang J, You P. (2013). The complete nucleotide sequence of mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae). Dong Wu Fen Lei Xue Bao 38:695–704. 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 GD, Chen IS, Zhu JQ, Shen CN. (2014). The complete mitochondrial genome of Chinese rod gugeon Abbottina rivularis (Cypriniformes, Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.905838. 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. Wang H, Li C, Yang XX, Yang SB, Han JW, He LP, Wei M, et al. (2013). Complete mitochondrial genome of Pseudobagrus ondon Shaw. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.834437. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2014). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.796461.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae) Heng Wang, Xiaoxue Yang, Xiarong Wang, Chen Li, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv & Pingping Huang To cite this article: Heng Wang, Xiaoxue Yang, Xiarong Wang, Chen Li, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv & Pingping Huang (2014): Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947596
Published online: 08 Aug 2014.
Submit your article to this journal
Article views: 18
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: [University of Lethbridge]
Date: 05 November 2015, At: 15:32
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947596
MITOGENOME ANNOUNCEMENT
Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae) Heng Wang*, Xiaoxue Yang*, Xiarong Wang*, Chen Li*, Jiangwen Gu, Shoubao Yang, Liping He, Sisi Lv, and Pingping Huang
Downloaded by [University of Lethbridge] at 15:32 05 November 2015
College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of Abbottina rivularis was determined; the phylogenetic analysis with other individuals and closely related species of the gudgeons was carried out. The complete mitogenome of A. rivularis was 16,597 bp in length, which consists of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 2 non-coding regions: (D-loop and OL). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%). This study provides useful data to genetics, conservation and evolution study of the gudgeons.
Abbottina rivularis, mitogenome, sequencing
Abbottina rivularis (Cypriniformes: Cyprinidae), is a small benthopelagic freshwater species of ray-finned fish in the family Cyprinidae. It is distributed widely in China, and also distributed in Korea and Japan. The mitochondrial genome sequence could provide useful information for genetics, conservation and evolution study of many aquatic species (Wang et al., 2013; Yang et al., 2014). Ten pairs of primers were used in this study, which were designed according to the complete mitochondrial genome sequence of A. rivularis (GenBank accession no. KF577979.1,
History Received 14 July 2014 Accepted 19 July 2014 Published online 8 August 2014
designated Ar-1) (He et al., 2013), which was a different individual of the same species that sampled from different places. PCR amplification was carried out in a total volume of 25 ml, including 60 ng template DNA, 1 U Taq DNA polymerase, 0.2 mM dNTP, 2 mM MgCl2, 20 pM of the sense and anti-sense primer each. The complete mitochondrial genome of A. rivularis (designated Ar-3) was sequenced and determined (16,597 bp in length, GenBank accession no. KM081703), which consists of 22 tRNA genes, 13 protein-coding genes (PCDs), 2 rRNA genes, and
Table 1. Organization of the mitochondrial genome of A. rivularis. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr
Abbreviations F 12S V 16S L nd1 I Q M nd2 W A N C Y
From 1 70 1024 1096 2784 2860 3838 3908 3980 4049 5094 5168 5238 5311 5342 5412
To 69 1023 1095 2783 2859 3834 3909 3978 4048 5093 5165 5236 5310 5341 5410 5482
Codon Size (bp) 69 954 72 1688 76 975 72 71 69 1045 72 69 73 31 69 71
Start
Stop
Amino acid
Anti-codon GAA TAC TAA
ATG
TAA
324 GAT TTG CAT
ATG
T– –
348 TCA TGC GTT GCA GTA
Intergenic nucleotide 0 0 0 0 0 3 2 1 0 0 2 1 0 0 1 1
Strand H H H H H H H L H H H L L L L
(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
Downloaded by [University of Lethbridge] at 15:32 05 November 2015
Locus 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
Abbreviations
From
To
Size (bp)
Start
Stop
Amino acid
cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
5484 7035 7109 7194 7885 7962 8120 8803 9587 9659 10,009 10,079 10,369 11,751 11,820 11,890 11,963 13,795 14,317 14,388 15,529 15,599 15,669
7034 7105 7180 7884 7960 8126 8803 9586 9658 10,008 10,078 10,375 11,750 11,819 11,888 11,962 13,798 14,316 14,385 15,528 15,599 15,668 16,597
1551 71 72 691 76 165 684 784 72 350 70 297 1382 69 69 73 1836 522 69 1141 71 70 929
GTG
TAA
516
Anti-codon 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
2 non-coding regions (Table 1). All of these genes were encoded on the heavy strand (H-strand), with the exception of one PCD (ND6) and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro; Table 1). All of the genes showed typical gene arrangement that similar to the vertebrate species (Jondeung & Karinthanyakit, 2010). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%) as that of other vertebrate mitochondrial genome. Phylogenetic tree was constructed based on the complete mitochondrial genome sequences of A. rivularis (GenBank accession no. KF577979.1, designated Ar-1; He et al., 2013), A. rivularis (GenBank accession no. KM081703, designated Ar-2) (Liu et al., 2014), A. rivularis (GenBank accession no. KM081703, designated Ar-3), Biwia springeri (GenBank accession no. AP011360.1) (Tang et al., 2011), Microphysogobio brevirostris (GenBank accession no. KF319122.1), and Romanogobio tenuicorpus (GenBank accession no. KF647873.1; Dong et al., 2014) using the neighbor-joining method (figure not shown). It showed that A. rivularis (Ar-3) is clustered with Ar-1 and Ar-2. This study provides useful data to genetics, conservation and evolution study of the gudgeons.
Declaration of interest This work was supported by the Public Welfare Project of Science Technology Department of Zhejiang province (2011C22084); Student Innovation Training Program of Shaoxing University (2014). The authors
TGT TGG
Intergenic nucleotide
Strand
0 3 13 0 1 7 1 0 0 0 0 7 0 0 1 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 –
report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Dong F, Tong GX, Kuang YY, Sun XW. (2014). Complete mitochondrial genome sequence of Romanogobio tenuicorpus (Amur white fin gudgeon). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.865169. He H, Wang J, You P. (2013). The complete nucleotide sequence of mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae). Dong Wu Fen Lei Xue Bao 38:695–704. 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 GD, Chen IS, Zhu JQ, Shen CN. (2014). The complete mitochondrial genome of Chinese rod gugeon Abbottina rivularis (Cypriniformes, Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2014.905838. 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. Wang H, Li C, Yang XX, Yang SB, Han JW, He LP, Wei M, et al. (2013). Complete mitochondrial genome of Pseudobagrus ondon Shaw. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.834437. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2014). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.796461.
