http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.953117
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Coregonus usssruensis Berg
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 06/23/15 For personal use only.
Shu-Qun Xue, Bo Ma, Xiao-Feng Zhang, Pei-Xian Luan, and Jian-Guo Lu National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, P. R. China Abstract
Keywords
The complete mitochondrial genome of Coregonus usssruens is was determined in this study. The mitogenome is 16,738 bp in length and contains 1D-loop region, 2 ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall base composition of the heavy strand is 26.79% for A, 29.45% for C, 18.10% for G and 25.66% for T. The percentage of G+C content is 47.55%. This is the first time of the mitochondrial genome sequencing for C. usssruensis.
Coregonus usssruensis, mitochondrial DNA, mitogenome history
Coregonus usssruensis belonging to Salmoniformes, Salmonidae, Coregoninae, Coregonus, inhabits in Heilongjiang and Wusuli River, is an important economic fish (Liang et al., 2004). However, its wild population has declined rapidly because of excess fishing and habitat destruction, and it was listed in RedCover Book by IUCN as endangered fishes in recent years (Ma et al., 2003). In this study, one adult was used for the complete mitochondrial DNA sequencing, which was collected from Fuyuan city in Heilongjiang Province of China. The total genomic DNA was extracted from alcohol-preserved fin using traditional the phenol-chloroform method (Taggart et al., 1992). 26 primers were used to amplify the target PCR products for the sequencing, designed by the Primer 3.0 online. The sequencing results were then assembled using ContigExpess 9.0 software (ContigExpress, New York, NY). The location of protein-coding genes were determined by comparing with the corresponding known sequences of other Coregonus fish species. Also the transfer RNA (tRNA) genes were identified using the program tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE). The complete mitochondrial genome length of C. usssruensis was 16,738 bp (GenBank accession number KM210289). It was consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and 1 D-loop region (Table 1). The overall base composition of the heavy strand was is 26.79% for A, 29.45% for C, 18.10% for G and 25.66% for T.
Correspondence: Jian-Guo Lu, National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 232 Hesong Street, Harbin 150070, P. R. China. Fax: +86-451-84604803. E-mail: [email protected]
History Received 1 August 2014 Accepted 6 August 2014 Published online 29 August 2014
Table 1. Organization of the mitochondrial genome of C. usssruensis. Position
Codon
Gene
From
To
Size(bp)
tRNAPre 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln TrnaMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis TrnaSer tRNALeu ND5 ND6 TrnaGlu CYTB
1 69 1016 1088 2766 2841 3823 3892 3962 4031 5082 5155 5225 5332 5401 5474 7026 7101 7189 7880 7955 8113 8796 9581 9651 10,000 10,071 10,361 11,742 11,811 11,881 11,954 13,789 14,311 14,383
68 1015 1087 2766 2840 3815 3894 3962 4030 5080 5153 5223 5297 5401 5472 7025 7096 7174 7879 7953 8122 8796 9580 9650 9999 10,070 10,367 11,741 11,810 11,879 11,953 13,792 14,310 14,378 15,523
68 947 72 1679 75 975 72 71 69 1050 72 69 73 70 72 1552 71 74 691 74 168 684 785 70 349 71 297 1381 69 69 73 1839 522 68 1140
Start
Stop
ATG
TAG
ATG
TAG
ATG
TAG
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATG
TAG
ATG ATG
TAG TAA
ATG ATG
TAA TAA
ATG
TAA
Strand 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
(continued )
2
S.-Q. Xue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene Thr
tRNA tRNAPro D-loop
Codon
From
To
Size(bp)
15,524 15,595 15,665
15,595 15,664 16,738
72 70 1074
Start
Stop
Strand H L H
T – represent incomplete stop codon.
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 06/23/15 For personal use only.
Declaration of interest This study was funded and supported by the grants from national infrastructure of fishery germplasm resources, the Special Scientific
Research Funds for Central Non-profit Institutes from Chinese Academy of Fishery Science (2013A0101), National Science Foundation of China (31302177), and Heilongjiang River Fisheries Research Institute Foundation (HSY201301). The authors have no conflicts of interest. The first author alone is responsible for the content and writing of the paper.
References Liang LQ, Chang YM, Dong CZ. (2004). Analysis of genetic diversity for Coregonus ussuriensis Berg in Heilongjiang River. J Fish Sci China 11: 501–5. Ma B, Shi LY, Dong CZ. (2003). Biochemical genetic structure in Coregonus ussuriensis Berg. J Fish Sci China 10:195–200. Taggart JB, Hynes RA, Prodoh PA, Ferguson A. (1992). A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40:963–5.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Coregonus usssruensis Berg
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 06/23/15 For personal use only.
Shu-Qun Xue, Bo Ma, Xiao-Feng Zhang, Pei-Xian Luan, and Jian-Guo Lu National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, P. R. China Abstract
Keywords
The complete mitochondrial genome of Coregonus usssruens is was determined in this study. The mitogenome is 16,738 bp in length and contains 1D-loop region, 2 ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall base composition of the heavy strand is 26.79% for A, 29.45% for C, 18.10% for G and 25.66% for T. The percentage of G+C content is 47.55%. This is the first time of the mitochondrial genome sequencing for C. usssruensis.
Coregonus usssruensis, mitochondrial DNA, mitogenome history
Coregonus usssruensis belonging to Salmoniformes, Salmonidae, Coregoninae, Coregonus, inhabits in Heilongjiang and Wusuli River, is an important economic fish (Liang et al., 2004). However, its wild population has declined rapidly because of excess fishing and habitat destruction, and it was listed in RedCover Book by IUCN as endangered fishes in recent years (Ma et al., 2003). In this study, one adult was used for the complete mitochondrial DNA sequencing, which was collected from Fuyuan city in Heilongjiang Province of China. The total genomic DNA was extracted from alcohol-preserved fin using traditional the phenol-chloroform method (Taggart et al., 1992). 26 primers were used to amplify the target PCR products for the sequencing, designed by the Primer 3.0 online. The sequencing results were then assembled using ContigExpess 9.0 software (ContigExpress, New York, NY). The location of protein-coding genes were determined by comparing with the corresponding known sequences of other Coregonus fish species. Also the transfer RNA (tRNA) genes were identified using the program tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/tRNAscan-SE). The complete mitochondrial genome length of C. usssruensis was 16,738 bp (GenBank accession number KM210289). It was consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and 1 D-loop region (Table 1). The overall base composition of the heavy strand was is 26.79% for A, 29.45% for C, 18.10% for G and 25.66% for T.
Correspondence: Jian-Guo Lu, National Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, 232 Hesong Street, Harbin 150070, P. R. China. Fax: +86-451-84604803. E-mail: [email protected]
History Received 1 August 2014 Accepted 6 August 2014 Published online 29 August 2014
Table 1. Organization of the mitochondrial genome of C. usssruensis. Position
Codon
Gene
From
To
Size(bp)
tRNAPre 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln TrnaMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis TrnaSer tRNALeu ND5 ND6 TrnaGlu CYTB
1 69 1016 1088 2766 2841 3823 3892 3962 4031 5082 5155 5225 5332 5401 5474 7026 7101 7189 7880 7955 8113 8796 9581 9651 10,000 10,071 10,361 11,742 11,811 11,881 11,954 13,789 14,311 14,383
68 1015 1087 2766 2840 3815 3894 3962 4030 5080 5153 5223 5297 5401 5472 7025 7096 7174 7879 7953 8122 8796 9580 9650 9999 10,070 10,367 11,741 11,810 11,879 11,953 13,792 14,310 14,378 15,523
68 947 72 1679 75 975 72 71 69 1050 72 69 73 70 72 1552 71 74 691 74 168 684 785 70 349 71 297 1381 69 69 73 1839 522 68 1140
Start
Stop
ATG
TAG
ATG
TAG
ATG
TAG
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATG
TAG
ATG ATG
TAG TAA
ATG ATG
TAA TAA
ATG
TAA
Strand 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
(continued )
2
S.-Q. Xue et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene Thr
tRNA tRNAPro D-loop
Codon
From
To
Size(bp)
15,524 15,595 15,665
15,595 15,664 16,738
72 70 1074
Start
Stop
Strand H L H
T – represent incomplete stop codon.
Mitochondrial DNA Downloaded from informahealthcare.com by Biblioteka Uniwersytetu Warszawskiego on 06/23/15 For personal use only.
Declaration of interest This study was funded and supported by the grants from national infrastructure of fishery germplasm resources, the Special Scientific
Research Funds for Central Non-profit Institutes from Chinese Academy of Fishery Science (2013A0101), National Science Foundation of China (31302177), and Heilongjiang River Fisheries Research Institute Foundation (HSY201301). The authors have no conflicts of interest. The first author alone is responsible for the content and writing of the paper.
References Liang LQ, Chang YM, Dong CZ. (2004). Analysis of genetic diversity for Coregonus ussuriensis Berg in Heilongjiang River. J Fish Sci China 11: 501–5. Ma B, Shi LY, Dong CZ. (2003). Biochemical genetic structure in Coregonus ussuriensis Berg. J Fish Sci China 10:195–200. Taggart JB, Hynes RA, Prodoh PA, Ferguson A. (1992). A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40:963–5.
