http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919459
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Pseudogyrinocheilus prochilus (Cypriniformes: Cyprinidae) Xingjian Yue, Jinrong Shi, and Yuanchao Zou
Mitochondrial DNA Downloaded from informahealthcare.com by University of Manitoba on 08/29/15 For personal use only.
Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, People’s Republic of China Abstract
Keywords
The complete mitochondrial sequence of Pseudogyrinocheilus prochilus, an endemic species to China and mainly distributed in upper Yangtze River and its tributaries, was obtained by PCR. It was 16,595 bp in length and comprised 37 mitochondrial genes (22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes) and 2 non-coding regions. The overall base composition of H-strand was 31.40% A, 26.78% C, 16.18% G, and 25.64% T. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The composition and order of mitochondrial gene have no unique characteristics compared to most of other fishes.
Complete mitochondrial genome, Labeoninae, Pseudogyrinocheilus prochilus
The subfamily Labeoninae contains around 40 genera and 400 species which are widely distributed in tropical rivers of Africa and Asia. Labeonins show a high degree of morphological modification and variation in their oromandibular structures (Yang et al., 2012; Zhang et al., 2008). There are some published complete mitochondrial genomes of Labeonini in Genbank. Some distinctive features were detected, such as tandem repeat noncoding region in Garra qiaojiensis (Xiong et al., 2014). Here, we determined the complete mitochondrial DNA sequence of Pseudogyrinocheilus prochilus which could contribute to better understand phylogeny of Labeonini. Pseudogyrinocheilus prochilus is an endemic species to China and mainly distributed in upper Yangtze River and its tributaries (Zhang et al., 2000). It prefers to inhabit swift currents and feed on algae and aquatic insect. It’s a commercial fish due to its good taste, rich nutrition (Ding, 1994). Because of heavy fishing, dam construction in the Yangtze River drainage, the wild populations have rapidly declined in recent years. The sample was collected in Chishui River (a tributary of Yangtze River) from Chishui County, Guizhou Province. The locations of genes were determined by comparing with the corresponding know sequences of other fishes.
Correspondence: Xingjian Yue, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, People’s Republic of China. Tel: +8608322344699. Fax: +8608322341862. E-mail: [email protected]
History Received 13 April 2014 Accepted 24 April 2014 Published online 27 May 2014
The complete mtDNA sequence of P. prochilus was 16,595 bp in length (GenBank Accession No. KJ684987), obtained by PCR and contains 37 mitochondrial genes: 13 protein-coding genes (ATP6, ATP8, CO1-3, ND1-6 and 4L, cyt b), 2 ribosomal RNAs (12S, 16S rRNA), 22 transfer RNA genes, 2 non-coding regions: origin of light-strand replication (OL) and control region (Table 1). The overall base composition of H-strand was 31.40% A, 26.78% C, 16.18% G, and 25.64% T with an A + T rich feature. Except for eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, tRNAPro) and one protein-coding gene (ND6), most of the genes were encoded on the H-strand. A total of 25 bp overlapped nucleotides were scattered. Eight overlaps in the pairs of genes ND2–tRNATrp, ATP8–ATP6, ATP6–COIII, COIII–tRNAGly, ND3–tRNAArg, ND4L–ND4, ND5–ND6, tRNAThr–tRNAPro ranged from 1 to 7 bp in length. Among the protein-coding genes, COI starts with codon GTG, and the remaining 12 genes have the common initiation codon ATG. Ten protein-coding genes end with complete stop codons TAA (ND1, COI, ATPase8, ATPase6, COIII, ND4L, ND5) and TAG (ND2, ND3, ND6), the rest three genes end with incomplete stop codons T (COII, ND4, cytb). The 12S and 16S rRNA genes were 954 and 1687 bp in length, respectively, and located between tRNAPhe and tRNALeu, separated by tRNAVal. The length of 22 tRNA genes ranged from 66 (tRNACys) to 76 bp (tRNALeu(UUR), tRNALys). The major non-coding region (control region) was located between tRNAPhe and tRNAPro and was 938 bp. The second non-coding region (OL) was located between the tRNAAsn and tRNACys and was 33 bp. The other 12 smaller non-coding fragments ranged from 1 to 13 bp leaving a total of 36 bp intergenic spacers. The composition and order of mitochondrial gene have no unique characteristics compared to most of other fishes.
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X. Yue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of P. procheilus. Size Locus
Mitochondrial DNA Downloaded from informahealthcare.com by University of Manitoba on 08/29/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn Rep origin tRNACys tRNATyr CO I tRNASer(UCN) tRNAAsp CO II tRNALys ATP8 ATP6 CO III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu cyt b tRNAThr tRNAPro Control region
Abb.
Position
Nucleotide (bp)
F 12S V 16S L nd1 I Q M nd2 W A N OL C Y co 1 S D co 2 K atp 8 atp 6 co 3 G nd 3 R nd4L ND4 H S L nd5 nd6 E cyt b T P CR
1–69 70–1023 1024–1095 1096–2781 2782–2857 2858–3832 3837–3908 3907–3976 3978–4046 4047–5093 5092–5162 5165–5233 5235–5307 5308–5340 5341–5406 5408–5478 5480–7030 7031–7101 7105–7176 7190–7880 7881–7956 7958–8122 8116–8799 8799–9584 9584–9655 9656–10,006 10,005–10,074 10,075–10,371 10,365–11,745 11,746–11,814 11,815–11,883 11,885–11,957 11,961–13,784 13,781–14,302 14,303–14,371 14,376–15,516 15,517–15,588 15,588–15,657 15,658–16,595
69 954 72 1687 76 975 72 70 69 1047 71 69 73 33 66 71 1551 71 72 691 76 165 684 786 72 351 70 297 1381 69 69 73 1824 522 69 1141 72 70 938
Codon Amono acid
Start
Stop
Anti-codon
Intergenic nucleotide
Strand
0 0 0 0 0 4 0 1 0 2 3 1 0 0 1 1 0 3 13 0 1 7 1 1 0 2 0 7 0 0 1 3 4 0 4 0 1 –
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 –
GAA TAC TAA 324
ATG
TAA GAT TTG CAT
348
ATG
TAG TCA TGC GTT GCA GTA
516
GTG
TAA TGA GTC
230
ATG
T– –
54 227 261
ATG ATG ATG
TAA TAA TAA
116
ATG
TAG
98 460
ATG ATG
TAA T– –
TTT
TCC TCG GTG GCT TAG 607 173
ATG ATG
TAA TAG
380
ATG
T– –
TTC TGT TGG
ATP 6 and 8, ATPase subunits 6 and 8. bp, base pair(s). COI–III, cytochrome c oxidase subunits I–III. cyt b, cytochrome b. ND1–6, 4L, NADH dehydrogenase subunits 1–6, 4L. tRNA, transfer RNA. 12SrRNA and 16S rRNA, 12S and 16S ribosomal RNA.
Declaration of interest The present work was supported by the science and technology fund from the Education Department of Sichuan Province, PR China (No. 12ZA246), and the science and technology fund from Science, Technology and Intellectual Property Bureau of Neijiang, Sichuan Province, PR China (No. 11028). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Ding R. (1994). The fishes of Sichuan, China (in Chinese). Chengdu, China: Sichuan Publishing House of Science and Technology.
Xiong H, Chen W, Gan X, Wang X. (2014). Complete sequence and rearrangement of the mitochondrial genome of Garra qiaojiensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.869682. Yang L, Arunachalam M, Sado T, Levin BA, Golubtsov AS, Freyhof J, Friel JP, et al. (2012). Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Mol Phylogenet Evol 65: 362–79. Zhang E, Xin Q, Lan J. (2008). Description of a new genus and two new species of Labeonine fishes from South China (Teleostei: Cyprinidae). Zootaxa 1682:33–44. Zhang E, Yue P, Chen J. (2000). Cyprinidae: Laleoninae. In: Yue P, editor. Fauna Sinica. Osteichthyes. Cypriniformes III (in Chinese). Beijing, China: Science Press. p 171–272.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Pseudogyrinocheilus prochilus (Cypriniformes: Cyprinidae) Xingjian Yue, Jinrong Shi, and Yuanchao Zou
Mitochondrial DNA Downloaded from informahealthcare.com by University of Manitoba on 08/29/15 For personal use only.
Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, People’s Republic of China Abstract
Keywords
The complete mitochondrial sequence of Pseudogyrinocheilus prochilus, an endemic species to China and mainly distributed in upper Yangtze River and its tributaries, was obtained by PCR. It was 16,595 bp in length and comprised 37 mitochondrial genes (22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes) and 2 non-coding regions. The overall base composition of H-strand was 31.40% A, 26.78% C, 16.18% G, and 25.64% T. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The composition and order of mitochondrial gene have no unique characteristics compared to most of other fishes.
Complete mitochondrial genome, Labeoninae, Pseudogyrinocheilus prochilus
The subfamily Labeoninae contains around 40 genera and 400 species which are widely distributed in tropical rivers of Africa and Asia. Labeonins show a high degree of morphological modification and variation in their oromandibular structures (Yang et al., 2012; Zhang et al., 2008). There are some published complete mitochondrial genomes of Labeonini in Genbank. Some distinctive features were detected, such as tandem repeat noncoding region in Garra qiaojiensis (Xiong et al., 2014). Here, we determined the complete mitochondrial DNA sequence of Pseudogyrinocheilus prochilus which could contribute to better understand phylogeny of Labeonini. Pseudogyrinocheilus prochilus is an endemic species to China and mainly distributed in upper Yangtze River and its tributaries (Zhang et al., 2000). It prefers to inhabit swift currents and feed on algae and aquatic insect. It’s a commercial fish due to its good taste, rich nutrition (Ding, 1994). Because of heavy fishing, dam construction in the Yangtze River drainage, the wild populations have rapidly declined in recent years. The sample was collected in Chishui River (a tributary of Yangtze River) from Chishui County, Guizhou Province. The locations of genes were determined by comparing with the corresponding know sequences of other fishes.
Correspondence: Xingjian Yue, Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University, Neijiang, People’s Republic of China. Tel: +8608322344699. Fax: +8608322341862. E-mail: [email protected]
History Received 13 April 2014 Accepted 24 April 2014 Published online 27 May 2014
The complete mtDNA sequence of P. prochilus was 16,595 bp in length (GenBank Accession No. KJ684987), obtained by PCR and contains 37 mitochondrial genes: 13 protein-coding genes (ATP6, ATP8, CO1-3, ND1-6 and 4L, cyt b), 2 ribosomal RNAs (12S, 16S rRNA), 22 transfer RNA genes, 2 non-coding regions: origin of light-strand replication (OL) and control region (Table 1). The overall base composition of H-strand was 31.40% A, 26.78% C, 16.18% G, and 25.64% T with an A + T rich feature. Except for eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, tRNAPro) and one protein-coding gene (ND6), most of the genes were encoded on the H-strand. A total of 25 bp overlapped nucleotides were scattered. Eight overlaps in the pairs of genes ND2–tRNATrp, ATP8–ATP6, ATP6–COIII, COIII–tRNAGly, ND3–tRNAArg, ND4L–ND4, ND5–ND6, tRNAThr–tRNAPro ranged from 1 to 7 bp in length. Among the protein-coding genes, COI starts with codon GTG, and the remaining 12 genes have the common initiation codon ATG. Ten protein-coding genes end with complete stop codons TAA (ND1, COI, ATPase8, ATPase6, COIII, ND4L, ND5) and TAG (ND2, ND3, ND6), the rest three genes end with incomplete stop codons T (COII, ND4, cytb). The 12S and 16S rRNA genes were 954 and 1687 bp in length, respectively, and located between tRNAPhe and tRNALeu, separated by tRNAVal. The length of 22 tRNA genes ranged from 66 (tRNACys) to 76 bp (tRNALeu(UUR), tRNALys). The major non-coding region (control region) was located between tRNAPhe and tRNAPro and was 938 bp. The second non-coding region (OL) was located between the tRNAAsn and tRNACys and was 33 bp. The other 12 smaller non-coding fragments ranged from 1 to 13 bp leaving a total of 36 bp intergenic spacers. The composition and order of mitochondrial gene have no unique characteristics compared to most of other fishes.
2
X. Yue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of P. procheilus. Size Locus
Mitochondrial DNA Downloaded from informahealthcare.com by University of Manitoba on 08/29/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn Rep origin tRNACys tRNATyr CO I tRNASer(UCN) tRNAAsp CO II tRNALys ATP8 ATP6 CO III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu cyt b tRNAThr tRNAPro Control region
Abb.
Position
Nucleotide (bp)
F 12S V 16S L nd1 I Q M nd2 W A N OL C Y co 1 S D co 2 K atp 8 atp 6 co 3 G nd 3 R nd4L ND4 H S L nd5 nd6 E cyt b T P CR
1–69 70–1023 1024–1095 1096–2781 2782–2857 2858–3832 3837–3908 3907–3976 3978–4046 4047–5093 5092–5162 5165–5233 5235–5307 5308–5340 5341–5406 5408–5478 5480–7030 7031–7101 7105–7176 7190–7880 7881–7956 7958–8122 8116–8799 8799–9584 9584–9655 9656–10,006 10,005–10,074 10,075–10,371 10,365–11,745 11,746–11,814 11,815–11,883 11,885–11,957 11,961–13,784 13,781–14,302 14,303–14,371 14,376–15,516 15,517–15,588 15,588–15,657 15,658–16,595
69 954 72 1687 76 975 72 70 69 1047 71 69 73 33 66 71 1551 71 72 691 76 165 684 786 72 351 70 297 1381 69 69 73 1824 522 69 1141 72 70 938
Codon Amono acid
Start
Stop
Anti-codon
Intergenic nucleotide
Strand
0 0 0 0 0 4 0 1 0 2 3 1 0 0 1 1 0 3 13 0 1 7 1 1 0 2 0 7 0 0 1 3 4 0 4 0 1 –
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 –
GAA TAC TAA 324
ATG
TAA GAT TTG CAT
348
ATG
TAG TCA TGC GTT GCA GTA
516
GTG
TAA TGA GTC
230
ATG
T– –
54 227 261
ATG ATG ATG
TAA TAA TAA
116
ATG
TAG
98 460
ATG ATG
TAA T– –
TTT
TCC TCG GTG GCT TAG 607 173
ATG ATG
TAA TAG
380
ATG
T– –
TTC TGT TGG
ATP 6 and 8, ATPase subunits 6 and 8. bp, base pair(s). COI–III, cytochrome c oxidase subunits I–III. cyt b, cytochrome b. ND1–6, 4L, NADH dehydrogenase subunits 1–6, 4L. tRNA, transfer RNA. 12SrRNA and 16S rRNA, 12S and 16S ribosomal RNA.
Declaration of interest The present work was supported by the science and technology fund from the Education Department of Sichuan Province, PR China (No. 12ZA246), and the science and technology fund from Science, Technology and Intellectual Property Bureau of Neijiang, Sichuan Province, PR China (No. 11028). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Ding R. (1994). The fishes of Sichuan, China (in Chinese). Chengdu, China: Sichuan Publishing House of Science and Technology.
Xiong H, Chen W, Gan X, Wang X. (2014). Complete sequence and rearrangement of the mitochondrial genome of Garra qiaojiensis (Cypriniformes: Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.869682. Yang L, Arunachalam M, Sado T, Levin BA, Golubtsov AS, Freyhof J, Friel JP, et al. (2012). Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Mol Phylogenet Evol 65: 362–79. Zhang E, Xin Q, Lan J. (2008). Description of a new genus and two new species of Labeonine fishes from South China (Teleostei: Cyprinidae). Zootaxa 1682:33–44. Zhang E, Yue P, Chen J. (2000). Cyprinidae: Laleoninae. In: Yue P, editor. Fauna Sinica. Osteichthyes. Cypriniformes III (in Chinese). Beijing, China: Science Press. p 171–272.
