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 complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae) Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu & Mei-hua Xiong To cite this article: Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu & Mei-hua Xiong (2014): The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971279
Published online: 16 Oct 2014.
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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: 05 November 2015, At: 13:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971279
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae) Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu, and Mei-hua Xiong
Downloaded by [NUS National University of Singapore] at 13:26 05 November 2015
Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, China Abstract
Keywords
In this study, the complete mitochondrial DNA genome sequence of Xenophysogobio nudicorpa was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of X. nudicorpa is a circular molecule of 16,616 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of X. nudicorpa is 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). The results could provide useful data for studying genetic diversity and phylogenetics in X. nudicorpa and related species.
Mitochondrial genome, resource management, Xenophysogobio nudicorpa
Xenophysogobio nudicorpa is a small freshwater fish belonging to the family of Cyprinidae, which is mainly distributed in the in the upper Yangtze River and its tributaries in China (Ding, 1994). To date, no genomic resources were available for X. nudicorpa. In this study, we reported the complete mitochondrial genome sequence of X. nudicorpa (GenBank accession number: KM516103), which would be useful for studying genetic diversity and phylogenetics in X. nudicorpa and related species. The sample was collected from Yibin section of the Yangtze River, Sichuan Province, China. In order to amplify the complete mitochondrial genome of X. nudicorpa, eighteen primers were generated using Primer Premier 5.0 (PREMIER Biosoft, Palo Alto, CA) based on Xenophysogobio boulengeri (GenBank accession number KJ641842). And they were used for polymerase chain reaction amplification and sequencing. After assembling and inspecting with software Vector NTI 11.5 (NY) the complete mitogenome of X. nudicorpa was obtained. Annotation of the mtDNA genome was executed by MitoAnnotator (Iwasaki et al., 2013) and nucleotide composition was calculated by MEGA6 (Tamura et al., 2013). The complete mitochondrial DNA sequence of X. nudicorpa was a circular molecule of 16,616 bp in length. It consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes and a non-coding
History Received 17 September 2014 Accepted 26 September 2014 Published online 16 October 2014
control region (D-loop; Table 1). Like other species in genus Gobiobotia, most mitochondrial genes were encoded on the H-strand except ND6 gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro). The overall nucleotides composition of the X. nudicorpa mtDNA was 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). Twelve proteincoding genes used ATG as the start codon, and COI began with GTG (Table 1). Five protein-coding genes terminated with the complete stop codons TAA (ND1, COI, ND4L, ND5, ND6), while the rest ended with an incomplete stop codon T (COII, ND3, ATPase 8, COIII and Cytb) or TA (ND2, ATPase 6, ND4), which is quite typical among mtDNA genes in other Gobiobotinae fishes (Hwang et al., 2013, 2014a,b). Sequence analyses displayed that two overlaps between tRNAs were found as follows: tRNAIle-tRNAGln, tRNAThr-tRNAPro. Two overlaps were also found between protein-coding genes (ATP8ATP6 and ND5-ND6; Table 1). The overlap of the ATPase genes are similar in most vertebrate mitochondrial genome and its size in fish (7–10 bp) is smaller than that in mammals (40–46 bp; Broughton et al., 2001). Overall, the complete mtDNA genome sequence obtained could be useful for studying genetic diversity and phylogenetics in X. nudicorpa and related species.
Correspondence: Mei-hua Xiong, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, 578 Xiongchu Avenue, Wuhan, 430079, China. Email: [email protected]
2
W.-T. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of X. nudicorpa. Position Gene
Downloaded by [NUS National University of Singapore] at 13:26 05 November 2015
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCN) tRNAAsp COII tRNALys ATPase 8 ATPase 6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
Size
From
To
Nucleotide (bp)
1 70 1033 1105 2795 2871 3849 3919 3991 4060 5106 5180 5250 5354 5423 5495 7046 7120 7205 7896 7973 8131 8814 9598 9670 10,019 10,088 10,387 11,760 11,829 11,899 11,972 13,804 14,326 14,399 15,540 15,611 15,681
69 1032 1104 2794 2870 3845 3920 3989 4059 5105 5177 5248 5322 5421 5493 7045 7116 7191 7895 7971 8137 8813 9597 9669 10,018 10,087 10,384 11,759 11,828 11,897 11,971 13,807 14,325 14,394 15,539 15,611 15,680 16,616
69 963 72 1690 76 975 72 71 69 1046 72 69 73 68 71 1551 71 72 691 76 165 683 784 72 349 69 297 1373 69 69 73 1836 522 69 1141 72 70 936
Codon Amino acid
Start
Stop*
324
ATG
TAA
348
ATG
TA–
516
GTG
TAA
230
ATG
T– –
54 227 261
ATG ATG ATG
T– – TA– T– –
116
ATG
T– –
98 460
ATG ATG
TAA TA–
607 173
ATG ATG
TAA TAA
380
ATG
T– –
Strandy
Intergenetic nucleotide (bp)
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L H H L
0 0 0 0 0 +3 2 +1 0 0 +2 +1 +31 +1 +1 0 +3 +13 0 +1 7 0 0 0 0 0 +2 0 0 +1 0 4 0 +4 0 1 0
Notes: *T– – or TA– represents incomplete stop codons; + Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotide. yH and L denote heavy and light strands, respectively.
Declaration of interest The work was supported by China Three Gorges Corporation Scientific Project (0799527). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Broughton RE, Milam JE, Roe BA. (2001). The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11: 1958–67. Ding R (ed). (1994). The fishes of Sichuan. Chengdu, Sichuan, China (in Chinese): Sichuan Publishing House of Science and Technology.
Hwang D-S, Byeon HK, Lee J-S. (2013). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia nakdongensis (Cypriniformes, Gobioninae). Mitochondrial DNA 24:409–10. Hwang D-S, Byeon HK, Lee J-S. (2014a). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia brevibarba (Cypriniformes; Cyprinidae). Mitochondrial DNA 25:33–4. Hwang D-S, Byeon HK, Lee J-S. (2014b). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia macrocephala (Cypriniformes; Cyprinidae). Mitochondrial DNA 25:31–2. 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. 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.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae) Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu & Mei-hua Xiong To cite this article: Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu & Mei-hua Xiong (2014): The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971279
Published online: 16 Oct 2014.
Submit your article to this journal
Article views: 6
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: [NUS National University of Singapore]
Date: 05 November 2015, At: 13:26
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971279
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Xenophysogobio nudicorpa (Cypriniformes; Cyprinidae) Wei-tao Li, Ke Shao, Shu-xiang Yan, Nian Xu, and Mei-hua Xiong
Downloaded by [NUS National University of Singapore] at 13:26 05 November 2015
Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, China Abstract
Keywords
In this study, the complete mitochondrial DNA genome sequence of Xenophysogobio nudicorpa was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of X. nudicorpa is a circular molecule of 16,616 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of X. nudicorpa is 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). The results could provide useful data for studying genetic diversity and phylogenetics in X. nudicorpa and related species.
Mitochondrial genome, resource management, Xenophysogobio nudicorpa
Xenophysogobio nudicorpa is a small freshwater fish belonging to the family of Cyprinidae, which is mainly distributed in the in the upper Yangtze River and its tributaries in China (Ding, 1994). To date, no genomic resources were available for X. nudicorpa. In this study, we reported the complete mitochondrial genome sequence of X. nudicorpa (GenBank accession number: KM516103), which would be useful for studying genetic diversity and phylogenetics in X. nudicorpa and related species. The sample was collected from Yibin section of the Yangtze River, Sichuan Province, China. In order to amplify the complete mitochondrial genome of X. nudicorpa, eighteen primers were generated using Primer Premier 5.0 (PREMIER Biosoft, Palo Alto, CA) based on Xenophysogobio boulengeri (GenBank accession number KJ641842). And they were used for polymerase chain reaction amplification and sequencing. After assembling and inspecting with software Vector NTI 11.5 (NY) the complete mitogenome of X. nudicorpa was obtained. Annotation of the mtDNA genome was executed by MitoAnnotator (Iwasaki et al., 2013) and nucleotide composition was calculated by MEGA6 (Tamura et al., 2013). The complete mitochondrial DNA sequence of X. nudicorpa was a circular molecule of 16,616 bp in length. It consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes and a non-coding
History Received 17 September 2014 Accepted 26 September 2014 Published online 16 October 2014
control region (D-loop; Table 1). Like other species in genus Gobiobotia, most mitochondrial genes were encoded on the H-strand except ND6 gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, and tRNAPro). The overall nucleotides composition of the X. nudicorpa mtDNA was 30.5% A, 26.0% C, 16.8% G, and 26.7% T, with a relatively high A+T content (57.2%). Twelve proteincoding genes used ATG as the start codon, and COI began with GTG (Table 1). Five protein-coding genes terminated with the complete stop codons TAA (ND1, COI, ND4L, ND5, ND6), while the rest ended with an incomplete stop codon T (COII, ND3, ATPase 8, COIII and Cytb) or TA (ND2, ATPase 6, ND4), which is quite typical among mtDNA genes in other Gobiobotinae fishes (Hwang et al., 2013, 2014a,b). Sequence analyses displayed that two overlaps between tRNAs were found as follows: tRNAIle-tRNAGln, tRNAThr-tRNAPro. Two overlaps were also found between protein-coding genes (ATP8ATP6 and ND5-ND6; Table 1). The overlap of the ATPase genes are similar in most vertebrate mitochondrial genome and its size in fish (7–10 bp) is smaller than that in mammals (40–46 bp; Broughton et al., 2001). Overall, the complete mtDNA genome sequence obtained could be useful for studying genetic diversity and phylogenetics in X. nudicorpa and related species.
Correspondence: Mei-hua Xiong, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, 578 Xiongchu Avenue, Wuhan, 430079, China. Email: [email protected]
2
W.-T. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of X. nudicorpa. Position Gene
Downloaded by [NUS National University of Singapore] at 13:26 05 November 2015
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCN) tRNAAsp COII tRNALys ATPase 8 ATPase 6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop
Size
From
To
Nucleotide (bp)
1 70 1033 1105 2795 2871 3849 3919 3991 4060 5106 5180 5250 5354 5423 5495 7046 7120 7205 7896 7973 8131 8814 9598 9670 10,019 10,088 10,387 11,760 11,829 11,899 11,972 13,804 14,326 14,399 15,540 15,611 15,681
69 1032 1104 2794 2870 3845 3920 3989 4059 5105 5177 5248 5322 5421 5493 7045 7116 7191 7895 7971 8137 8813 9597 9669 10,018 10,087 10,384 11,759 11,828 11,897 11,971 13,807 14,325 14,394 15,539 15,611 15,680 16,616
69 963 72 1690 76 975 72 71 69 1046 72 69 73 68 71 1551 71 72 691 76 165 683 784 72 349 69 297 1373 69 69 73 1836 522 69 1141 72 70 936
Codon Amino acid
Start
Stop*
324
ATG
TAA
348
ATG
TA–
516
GTG
TAA
230
ATG
T– –
54 227 261
ATG ATG ATG
T– – TA– T– –
116
ATG
T– –
98 460
ATG ATG
TAA TA–
607 173
ATG ATG
TAA TAA
380
ATG
T– –
Strandy
Intergenetic nucleotide (bp)
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L H H L
0 0 0 0 0 +3 2 +1 0 0 +2 +1 +31 +1 +1 0 +3 +13 0 +1 7 0 0 0 0 0 +2 0 0 +1 0 4 0 +4 0 1 0
Notes: *T– – or TA– represents incomplete stop codons; + Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotide. yH and L denote heavy and light strands, respectively.
Declaration of interest The work was supported by China Three Gorges Corporation Scientific Project (0799527). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Broughton RE, Milam JE, Roe BA. (2001). The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11: 1958–67. Ding R (ed). (1994). The fishes of Sichuan. Chengdu, Sichuan, China (in Chinese): Sichuan Publishing House of Science and Technology.
Hwang D-S, Byeon HK, Lee J-S. (2013). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia nakdongensis (Cypriniformes, Gobioninae). Mitochondrial DNA 24:409–10. Hwang D-S, Byeon HK, Lee J-S. (2014a). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia brevibarba (Cypriniformes; Cyprinidae). Mitochondrial DNA 25:33–4. Hwang D-S, Byeon HK, Lee J-S. (2014b). Complete mitochondrial genome of the freshwater gudgeon, Gobiobotia macrocephala (Cypriniformes; Cyprinidae). Mitochondrial DNA 25:31–2. 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. 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.
