http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.982584
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Xenophysogobio nudicorpa (Teleostei, Cypriniformes, Cyprinidae) Xiaoyun Zeng, Tian Huiwu, Dengqiang Wang, Xinbin Duan, and Daqing Chen
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/06/15 For personal use only.
Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, People’s Republic of China
Abstract
Keywords
Xenophysogobio nudicorpa is a rare and endemic fish species found only in the upper Yangtze River basin in China. Here, the complete mitochondrial genome of X. nudicorpa ha been determined by polymerase chain reaction and directly sequenced with primer walking method. The genome was 16,592 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding control region (D-loop). The gene order and composition of X. nudicorpa was similar to most other vertebrates. The overall base composition of the heavy strand was 30.22% A, 27.09% T, 25.76% C and 16.93% G, with a slight AT bias of 57.31%. The complete mitogenome sequence of X. nudicorpa provides fundamental data for further conversation genetics and captive breeding studies on this species.
Conversation genetics, cyprinidae, mitogenome, Yangtze River
Xenophysogobio nudicorpa (Teleostei, Cypriniformes, Cyprinidae) belongs to Cyprinidae family, which is rare and endemic to China. It is only distributed in the upper Yangtze River basin in China. Previous studies showed that no complete mitochondrial genomes in Xenophysogobio genera have been identified. Thus, we present the complete mitochondrial genome of X. nudicorpa, the first complete sequence from a member of the Xenophysogobio genera. The complete mitochondrial
History Received 11 October 2014 Accepted 27 October 2014 Published online 4 February 2015
DNA (mtDNA) sequence of X. nudicorpa can contribute to elucidate the evolutionary mechanisms and biogeography of Xenophysogobio and is useful for stock evaluation and conservation genetics for X. nudicorpa. In this study, 16 pairs of primers were used for polymerase chain reaction (PCR) amplification. Sequences were amplified according to previous studies (Wang et al., 2013). The PCR products were purified and then sequenced with the same primers
Table 1 Organization of the complete mitochondrial genome in X. nudicorpa.
Gene element tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COI tRNA-Ser(UCN) tRNA-Asp COII
Position
Overlap( ) Space(+)
Length (bp)
1–69 70–1032 1033–1104 1105–2794 2795–2870 2871–3845 3849–3918 3919–3989 3991–4059 4060–5105 5106–5177 5180–5248 5250–5322 5354–5421 5423–5493 5495–7045 7046–7116 7120–7191 7205–7895
0 0 0 0 0 0 3(+) 0 1(+) 0 0 2(+) 1(+) 31(+) 1(+) 1(+) 0 3(+) 13(+)
69 963 72 1690 76 975 70 71 69 1046 72 69 73 68 71 1551 71 72 691
Start codon
Stop codon
ATG
TAA
ATG
TA
GTG
TAA
ATG
T
Strand H H H H H H H L H H H L L L L H L H H (continued )
Correspondence: Daqing Chen, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, No.8, 1st Wudayuan Road, East Lake Hi-Tech Development Zone, Wuhan 430223, Hubei, People’s Republic of China. Tel/Fax: +86-027-81780058. E-mail: [email protected]
2
X. Zeng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1 Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/06/15 For personal use only.
Gene element tRNA-Lys ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
Position
Overlap( ) Space(+)
Length (bp)
7896–7971 7973–8137 8131–8814 8814–9597 9598–9669 9670–10,018 10,019–10,087 10,088–10,384 10,378–11,759 11,760–11,828 11,830–11,896 11,899–11,971 11,972–13,807 13804–14,325 14,326–14,394 14,399–15,539 15,539–15,610 15,611–15,680 15,681–16,592
0 1(+) 7( ) 1( ) 0 0 0 0 7( ) 0 1(+) 2(+) 0 4( ) 0 4(+) 1( ) 0 0
76 165 684 784 72 349 69 297 1382 69 67 73 1836 522 69 1141 72 70 912
as those used for PCR. After assembly and alignment, the mitogenome was annotated with MITOS (Bernt et al., 2012). Then, the complete mitochondrial genome sequence of X. nudicorpa was submitted and deposited in GenBank database with accession number KM373519. The overall nucleotide base composition is as follows: A, 30.45%; C, 26.03%; G, 16.85% and T, 26.67%, respectively, and the A + T content of the entire mtDNA sequence of X. nudicorpa was 57.12%, showing a slight AT bias commonly as in teleost fishes (Zhu et al., 2013). In addition, the mitogenome contents included 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 non-coding region (Table 1), which again are in accordance with those of other reported bony fishes (Chen et al., 2012). As in other vertebrates, most genes were encoded on the H-strand, except for the ND6 and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro), which were encoded on the L-strand, showing the typical gene arrangement conforming to the vertebrate consensus (Qiao et al., 2012). Four overlaps were detected between the protein coding genes as shown in ATP8– ATP6, ATP6–COIII, ND4L–ND4, and ND5–ND6 (Table 1). These overlaps are common 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). As shown in Table 1, except for COI, which began with GTG as an initiation codon, all others started with a standard codon ATG. However, the termination codons of the 13 protein-coding genes are varied (Table 1). Except for the detected complete stop codon TAA in open reading frames of X. nudicorpa, the two genes ND2 and ND4, and other four genes COII, COIII, ND3 and Cytb
Start codon
Stop codon
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA TA
ATG ATG
TAA TAA
ATG
T
Strand H H H H H H H H H H H H H L L H H L H
have an incomplete stop codon TA and T, respectively (Table 1). The control region (known as D-loop) is located between tRNAPro and tRNAPhe with 912 bp in length.
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 grants from China Three Gorges Corporation (Project NO.0799527).
References Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6. 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. Chen Y, Cheng QQ, Qiao HY, Zhu YX, Chen WM. (2012). The complete mitochondrial genome sequence of Rastrelliger kanagurta (Perciformes: Scombridae). Mitochondr DNA 24:114–16. Qiao HY, Cheng QQ, Chen Y, Chen WM, Zhu YX. (2012). The complete mitochondrial genome sequence of Coilia ectenes (Clupeiformes: Engraulidae). Mitochondrial DNA 24:123–5. Wang B, Ji P, Xu J, Sun J, Yang J, Xu P, Sun X. (2013). Complete mitochondrial genome of Leuciscus waleckii (Cypriniformes: Cyprinidae: Leuciscus). Mitochondrial DNA 24:126–8. Zhu YX, Chen Y, Cheng QQ, Qiao HY, Chen WM. (2013). The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes:Cyprinidae). Mitochondrial DNA 24:237–9.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Xenophysogobio nudicorpa (Teleostei, Cypriniformes, Cyprinidae) Xiaoyun Zeng, Tian Huiwu, Dengqiang Wang, Xinbin Duan, and Daqing Chen
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/06/15 For personal use only.
Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, People’s Republic of China
Abstract
Keywords
Xenophysogobio nudicorpa is a rare and endemic fish species found only in the upper Yangtze River basin in China. Here, the complete mitochondrial genome of X. nudicorpa ha been determined by polymerase chain reaction and directly sequenced with primer walking method. The genome was 16,592 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding control region (D-loop). The gene order and composition of X. nudicorpa was similar to most other vertebrates. The overall base composition of the heavy strand was 30.22% A, 27.09% T, 25.76% C and 16.93% G, with a slight AT bias of 57.31%. The complete mitogenome sequence of X. nudicorpa provides fundamental data for further conversation genetics and captive breeding studies on this species.
Conversation genetics, cyprinidae, mitogenome, Yangtze River
Xenophysogobio nudicorpa (Teleostei, Cypriniformes, Cyprinidae) belongs to Cyprinidae family, which is rare and endemic to China. It is only distributed in the upper Yangtze River basin in China. Previous studies showed that no complete mitochondrial genomes in Xenophysogobio genera have been identified. Thus, we present the complete mitochondrial genome of X. nudicorpa, the first complete sequence from a member of the Xenophysogobio genera. The complete mitochondrial
History Received 11 October 2014 Accepted 27 October 2014 Published online 4 February 2015
DNA (mtDNA) sequence of X. nudicorpa can contribute to elucidate the evolutionary mechanisms and biogeography of Xenophysogobio and is useful for stock evaluation and conservation genetics for X. nudicorpa. In this study, 16 pairs of primers were used for polymerase chain reaction (PCR) amplification. Sequences were amplified according to previous studies (Wang et al., 2013). The PCR products were purified and then sequenced with the same primers
Table 1 Organization of the complete mitochondrial genome in X. nudicorpa.
Gene element tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUR) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COI tRNA-Ser(UCN) tRNA-Asp COII
Position
Overlap( ) Space(+)
Length (bp)
1–69 70–1032 1033–1104 1105–2794 2795–2870 2871–3845 3849–3918 3919–3989 3991–4059 4060–5105 5106–5177 5180–5248 5250–5322 5354–5421 5423–5493 5495–7045 7046–7116 7120–7191 7205–7895
0 0 0 0 0 0 3(+) 0 1(+) 0 0 2(+) 1(+) 31(+) 1(+) 1(+) 0 3(+) 13(+)
69 963 72 1690 76 975 70 71 69 1046 72 69 73 68 71 1551 71 72 691
Start codon
Stop codon
ATG
TAA
ATG
TA
GTG
TAA
ATG
T
Strand H H H H H H H L H H H L L L L H L H H (continued )
Correspondence: Daqing Chen, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, No.8, 1st Wudayuan Road, East Lake Hi-Tech Development Zone, Wuhan 430223, Hubei, People’s Republic of China. Tel/Fax: +86-027-81780058. E-mail: [email protected]
2
X. Zeng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1 Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/06/15 For personal use only.
Gene element tRNA-Lys ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGY) tRNA-Leu(CUN) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
Position
Overlap( ) Space(+)
Length (bp)
7896–7971 7973–8137 8131–8814 8814–9597 9598–9669 9670–10,018 10,019–10,087 10,088–10,384 10,378–11,759 11,760–11,828 11,830–11,896 11,899–11,971 11,972–13,807 13804–14,325 14,326–14,394 14,399–15,539 15,539–15,610 15,611–15,680 15,681–16,592
0 1(+) 7( ) 1( ) 0 0 0 0 7( ) 0 1(+) 2(+) 0 4( ) 0 4(+) 1( ) 0 0
76 165 684 784 72 349 69 297 1382 69 67 73 1836 522 69 1141 72 70 912
as those used for PCR. After assembly and alignment, the mitogenome was annotated with MITOS (Bernt et al., 2012). Then, the complete mitochondrial genome sequence of X. nudicorpa was submitted and deposited in GenBank database with accession number KM373519. The overall nucleotide base composition is as follows: A, 30.45%; C, 26.03%; G, 16.85% and T, 26.67%, respectively, and the A + T content of the entire mtDNA sequence of X. nudicorpa was 57.12%, showing a slight AT bias commonly as in teleost fishes (Zhu et al., 2013). In addition, the mitogenome contents included 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 non-coding region (Table 1), which again are in accordance with those of other reported bony fishes (Chen et al., 2012). As in other vertebrates, most genes were encoded on the H-strand, except for the ND6 and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro), which were encoded on the L-strand, showing the typical gene arrangement conforming to the vertebrate consensus (Qiao et al., 2012). Four overlaps were detected between the protein coding genes as shown in ATP8– ATP6, ATP6–COIII, ND4L–ND4, and ND5–ND6 (Table 1). These overlaps are common 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). As shown in Table 1, except for COI, which began with GTG as an initiation codon, all others started with a standard codon ATG. However, the termination codons of the 13 protein-coding genes are varied (Table 1). Except for the detected complete stop codon TAA in open reading frames of X. nudicorpa, the two genes ND2 and ND4, and other four genes COII, COIII, ND3 and Cytb
Start codon
Stop codon
ATG ATG ATG
TAA TAA T
ATG
T
ATG ATG
TAA TA
ATG ATG
TAA TAA
ATG
T
Strand H H H H H H H H H H H H H L L H H L H
have an incomplete stop codon TA and T, respectively (Table 1). The control region (known as D-loop) is located between tRNAPro and tRNAPhe with 912 bp in length.
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 grants from China Three Gorges Corporation (Project NO.0799527).
References Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2012). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 7:00332–6. 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. Chen Y, Cheng QQ, Qiao HY, Zhu YX, Chen WM. (2012). The complete mitochondrial genome sequence of Rastrelliger kanagurta (Perciformes: Scombridae). Mitochondr DNA 24:114–16. Qiao HY, Cheng QQ, Chen Y, Chen WM, Zhu YX. (2012). The complete mitochondrial genome sequence of Coilia ectenes (Clupeiformes: Engraulidae). Mitochondrial DNA 24:123–5. Wang B, Ji P, Xu J, Sun J, Yang J, Xu P, Sun X. (2013). Complete mitochondrial genome of Leuciscus waleckii (Cypriniformes: Cyprinidae: Leuciscus). Mitochondrial DNA 24:126–8. Zhu YX, Chen Y, Cheng QQ, Qiao HY, Chen WM. (2013). The complete mitochondrial genome sequence of Schizothorax macropogon (Cypriniformes:Cyprinidae). Mitochondrial DNA 24:237–9.
