http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908357
MITOGENOME ANNOUNCEMENT
Complete mitochondrial DNA genome of Pseudobagrus medianalis (Siluriformes: Bagridae) Hong-wei Liang1,2, Zhong Li1, Gui-wei Zou1, and Ming-yan Shi3 Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China, 2Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, China, P.R. China, and 3College of Life Science, Luoyang Normal University, Luoyang, China, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Calgary on 02/04/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome was sequenced from the freshwater fish, Pseudobagrus medianalis (Siluriformes: Bagridae) in this study. The genome sequence was 16,647 bp in length, and the gene order and contents were identical with the bagridae fishes. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding regions (control region and origin of light-strand replication). All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition is 25.7% A, 30.9% T, 28.0% G, 15.4% C, with an A+T bias of 56.6%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
Bagridae, mitochondrial genome, Pseudobagrus medianalis, Siluriformes
Pseudobagrus medianalis which belongs to the family of Bagridae, is one of the Endangered fishes in Lake Dianchi, Yunnan, China (Chen et al., 2008). It was found throughout Lake Dianchi basin, including in the lake body, streams and headwater spring in the past (Chen et al., 2008). The natural resources of P. medianalis have decreased sharply because of water pollution, lake eutrophication and environment deterioration (Yan et al., 2012). At present it lives only in a few springs and effluent streams of the lake, such as White Dragon Spring, Black Dragon Sporing, Luo Dragon River and Longwangtang Spring (Chen et al., 2008; Yan et al., 2012). The complete mitogenome sequences of Pseudobagrus medianalis (KJ507136) was successfully sequenced, which was 16,647 bp in length. Similar of other Bagridae varieties such as Pelteobagrus fulvidraco (Liang et al., 2012) and Pseudobagrus brevicaudatus (Liang et al., 2013), the mitochondrial genome of
History Received 6 March 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 14 April 2014
P. medianalis comprised of 37 genes including 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Except for the ND6 gene and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNASer, tRNA-Glu and tRNA-Pro), all other genes were encoded on the heavy strand. The P. medianalis mitogenome was biased toward A+T nucleotides (56.6%). The overall base composition is 25.7% A, 30.9% T, 28.0% G, 15.4% C. The size and positioning of all protein-coding genes in P. medianalis were consistent with those of the other catfishes (Liang et al., 2012, 2013). As showed in Table 1, all these protein-coding genes sequences begin with an ATG start codon except for COX1 (started with GTG codon). The stop codons of 13 protein-coding genes of P. medianalis were used with TAA and T, which is quite typical among mtDNA genes present in other fishes (Kartavtsev et al., 2007; Nagase et al., 2005). There were seven protein-coding genes (ND1, COX1,
Table 1. Characteristics of the mitochondrial genome of P. medianalis. Position Gene tRNAPhe 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle
From 1 71 1140 1212 2890 2965 3944
Size To
70 1139 1211 2889 2964 3939 4017
Nucleotide (bp) 70 1069 72 1678 75 975 74
Codon Amino acid
324
Start
ATG
Stop*
TAA
Strand
Intergenetic Nucleotide+ (bp)
H H H H H H H
0 0 0 0 0 +4 (continued )
Correspondence: Gui-wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 430223, P.R. China. Tel/Fax: +86 2781780088. E-mail: [email protected]
2
H.-Wei Liang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Calgary on 02/04/15 For personal use only.
Position
Size
Gene
From
To
Nucleotide (bp)
tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATPase8 Atpase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
4016 4086 4156 5201 5274 5344 5449 5516 5588 7139 7214 7301 7992 8067 8225 8908 9692 9765 10,114 10,185 10,475 11,856 11,926 11,996 12,069 13,892 14,408 14,479 15,617 15,688 15,758
4086 4155 5200 5271 5342 5416 5515 5586 7138 7209 7286 7991 8065 8234 8908 9691 9764 10,113 10,184 10,481 11,855 11,925 11,992 12,068 13,895 14,407 14,477 15,616 15,689 15,757 16,647
71 70 1045 71 69 73 67 71 1551 71 73 691 74 168 684 784 73 349 71 297 1381 70 67 73 1827 516 70 1138 73 70 890
Codon Amino acid
Start
Stop*
348
ATG
T- -
516
GTG
TAA
230
ATG
T- -
55 227 261
ATG ATG ATG
TAA TAA T- -
116
ATG
T- -
98 460
ATG ATG
TAA T- -
608 171
ATG ATG
TAA TAA
379
ATG
T- -
Strand 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
Intergenetic Nucleotide+ (bp) 2 1 0 0 +2 +1 +32 0 +1 0 +4 +14 0 +1 10 1 0 0 0 0 7 0 0 +3 0 4 0 +1 0 2 0
*T- -: represent incomplete stop codons, +ve Numbers correspond to the nucleotides separating adjacent genes. –ve Numbers indicate overlapping nucleotides.
ATPase8, ATPase6, ND4L, ND5 and ND6) with TAA codon, while the other six genes (ND2, COX2, COX3, ND3, ND4 and Cytb) have the incomplete stop codon T. There were some overlapping structures between adjacent tRNA genes in the mitogenomes of P. medianalis. The 12S rRNA and 16S rRNA genes in P. medianalis mtDNA were 1069 bp and 1678 bp, respectively. The sequence analysis revealed that there were 22 tRNA genes in P. medianalis mitogenome. They were dispersed in the genome and ranged from 67 bp to 75 bp nucleotides in size. The major non-coding sequence of the P. medianalis mitochondrial genome is the control region (also known as D-loop), which was located between the tRNA-Pro and tRNA-Phe genes with 890 bp in length. The conserved sequence at D-Loop control region of P. medianalis are similar to the ones in others catfishes (Liang et al., 2013). OL was located between tRNA-Asn and tRNA-Cys, and was 32 bp in length.
Acknowledgements We are grateful to Dr. Dengqiang Wang from Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science for her assistance in sample collection.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The research was
supported by Special Basic Work Fund of Science and Technology (2013FY110700), Special Scientific Research Funds for Central Nonprofit Institutes, Chinese Academy of Fishery Sciences (2014A11JC05) and National S&T Infrastructure Platform of China.
References Chen XY, Cui GH, Yang JX. (2008). Threatened fishes of the word: Pseudobagrus medianalis (Regan) 1904 (Bagridae). Environ Biol Fish 81:253–4. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cytb and 16S rRNA genes. Gene 396:13–27. Liang HW, Hu GF, Li Z, Zou GW, Liu XL. (2012). Mitochondrial DNA sequence of yellow catfish (Pelteobagrus fulvidraco). Mitochondrial DNA 23:170–2. Liang HW, Meng Y, Li Z, Zhang Y, Zou GW. (2013). Complete mitochondrial DNA genome of pseudobagrus brevicaudatus (Siluriformes: Bagridae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.792060. Nagase M, Aimi T, Suginaka K, Kitamoto Y, Morinaga T. (2005). Complete mitochondrial DNA sequence of the Japanese flying fish Cypselurus hiraii. Fish Sci 71:914–23. Yan H, Xue CJ, Dong WH, Yang RL, Tu SH. (2012). Preliminary study on biological characteristics of DianChi Lake Bullheas species. Southwest China J Agri Sci 25:2376–9.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial DNA genome of Pseudobagrus medianalis (Siluriformes: Bagridae) Hong-wei Liang1,2, Zhong Li1, Gui-wei Zou1, and Ming-yan Shi3 Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China, 2Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, China, P.R. China, and 3College of Life Science, Luoyang Normal University, Luoyang, China, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Calgary on 02/04/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome was sequenced from the freshwater fish, Pseudobagrus medianalis (Siluriformes: Bagridae) in this study. The genome sequence was 16,647 bp in length, and the gene order and contents were identical with the bagridae fishes. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding regions (control region and origin of light-strand replication). All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition is 25.7% A, 30.9% T, 28.0% G, 15.4% C, with an A+T bias of 56.6%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
Bagridae, mitochondrial genome, Pseudobagrus medianalis, Siluriformes
Pseudobagrus medianalis which belongs to the family of Bagridae, is one of the Endangered fishes in Lake Dianchi, Yunnan, China (Chen et al., 2008). It was found throughout Lake Dianchi basin, including in the lake body, streams and headwater spring in the past (Chen et al., 2008). The natural resources of P. medianalis have decreased sharply because of water pollution, lake eutrophication and environment deterioration (Yan et al., 2012). At present it lives only in a few springs and effluent streams of the lake, such as White Dragon Spring, Black Dragon Sporing, Luo Dragon River and Longwangtang Spring (Chen et al., 2008; Yan et al., 2012). The complete mitogenome sequences of Pseudobagrus medianalis (KJ507136) was successfully sequenced, which was 16,647 bp in length. Similar of other Bagridae varieties such as Pelteobagrus fulvidraco (Liang et al., 2012) and Pseudobagrus brevicaudatus (Liang et al., 2013), the mitochondrial genome of
History Received 6 March 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 14 April 2014
P. medianalis comprised of 37 genes including 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Except for the ND6 gene and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNASer, tRNA-Glu and tRNA-Pro), all other genes were encoded on the heavy strand. The P. medianalis mitogenome was biased toward A+T nucleotides (56.6%). The overall base composition is 25.7% A, 30.9% T, 28.0% G, 15.4% C. The size and positioning of all protein-coding genes in P. medianalis were consistent with those of the other catfishes (Liang et al., 2012, 2013). As showed in Table 1, all these protein-coding genes sequences begin with an ATG start codon except for COX1 (started with GTG codon). The stop codons of 13 protein-coding genes of P. medianalis were used with TAA and T, which is quite typical among mtDNA genes present in other fishes (Kartavtsev et al., 2007; Nagase et al., 2005). There were seven protein-coding genes (ND1, COX1,
Table 1. Characteristics of the mitochondrial genome of P. medianalis. Position Gene tRNAPhe 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle
From 1 71 1140 1212 2890 2965 3944
Size To
70 1139 1211 2889 2964 3939 4017
Nucleotide (bp) 70 1069 72 1678 75 975 74
Codon Amino acid
324
Start
ATG
Stop*
TAA
Strand
Intergenetic Nucleotide+ (bp)
H H H H H H H
0 0 0 0 0 +4 (continued )
Correspondence: Gui-wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan 430223, P.R. China. Tel/Fax: +86 2781780088. E-mail: [email protected]
2
H.-Wei Liang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by University of Calgary on 02/04/15 For personal use only.
Position
Size
Gene
From
To
Nucleotide (bp)
tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATPase8 Atpase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
4016 4086 4156 5201 5274 5344 5449 5516 5588 7139 7214 7301 7992 8067 8225 8908 9692 9765 10,114 10,185 10,475 11,856 11,926 11,996 12,069 13,892 14,408 14,479 15,617 15,688 15,758
4086 4155 5200 5271 5342 5416 5515 5586 7138 7209 7286 7991 8065 8234 8908 9691 9764 10,113 10,184 10,481 11,855 11,925 11,992 12,068 13,895 14,407 14,477 15,616 15,689 15,757 16,647
71 70 1045 71 69 73 67 71 1551 71 73 691 74 168 684 784 73 349 71 297 1381 70 67 73 1827 516 70 1138 73 70 890
Codon Amino acid
Start
Stop*
348
ATG
T- -
516
GTG
TAA
230
ATG
T- -
55 227 261
ATG ATG ATG
TAA TAA T- -
116
ATG
T- -
98 460
ATG ATG
TAA T- -
608 171
ATG ATG
TAA TAA
379
ATG
T- -
Strand 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
Intergenetic Nucleotide+ (bp) 2 1 0 0 +2 +1 +32 0 +1 0 +4 +14 0 +1 10 1 0 0 0 0 7 0 0 +3 0 4 0 +1 0 2 0
*T- -: represent incomplete stop codons, +ve Numbers correspond to the nucleotides separating adjacent genes. –ve Numbers indicate overlapping nucleotides.
ATPase8, ATPase6, ND4L, ND5 and ND6) with TAA codon, while the other six genes (ND2, COX2, COX3, ND3, ND4 and Cytb) have the incomplete stop codon T. There were some overlapping structures between adjacent tRNA genes in the mitogenomes of P. medianalis. The 12S rRNA and 16S rRNA genes in P. medianalis mtDNA were 1069 bp and 1678 bp, respectively. The sequence analysis revealed that there were 22 tRNA genes in P. medianalis mitogenome. They were dispersed in the genome and ranged from 67 bp to 75 bp nucleotides in size. The major non-coding sequence of the P. medianalis mitochondrial genome is the control region (also known as D-loop), which was located between the tRNA-Pro and tRNA-Phe genes with 890 bp in length. The conserved sequence at D-Loop control region of P. medianalis are similar to the ones in others catfishes (Liang et al., 2013). OL was located between tRNA-Asn and tRNA-Cys, and was 32 bp in length.
Acknowledgements We are grateful to Dr. Dengqiang Wang from Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science for her assistance in sample collection.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The research was
supported by Special Basic Work Fund of Science and Technology (2013FY110700), Special Scientific Research Funds for Central Nonprofit Institutes, Chinese Academy of Fishery Sciences (2014A11JC05) and National S&T Infrastructure Platform of China.
References Chen XY, Cui GH, Yang JX. (2008). Threatened fishes of the word: Pseudobagrus medianalis (Regan) 1904 (Bagridae). Environ Biol Fish 81:253–4. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cytb and 16S rRNA genes. Gene 396:13–27. Liang HW, Hu GF, Li Z, Zou GW, Liu XL. (2012). Mitochondrial DNA sequence of yellow catfish (Pelteobagrus fulvidraco). Mitochondrial DNA 23:170–2. Liang HW, Meng Y, Li Z, Zhang Y, Zou GW. (2013). Complete mitochondrial DNA genome of pseudobagrus brevicaudatus (Siluriformes: Bagridae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.792060. Nagase M, Aimi T, Suginaka K, Kitamoto Y, Morinaga T. (2005). Complete mitochondrial DNA sequence of the Japanese flying fish Cypselurus hiraii. Fish Sci 71:914–23. Yan H, Xue CJ, Dong WH, Yang RL, Tu SH. (2012). Preliminary study on biological characteristics of DianChi Lake Bullheas species. Southwest China J Agri Sci 25:2376–9.
