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
Complete mitochondrial genome of Esox reichertii (Amur pike) Yu Liu & Jun Yang To cite this article: Yu Liu & Jun Yang (2015) Complete mitochondrial genome of Esox reichertii (Amur pike), Mitochondrial DNA, 26:6, 927-928, DOI: 10.3109/19401736.2013.863294 To link to this article: http://dx.doi.org/10.3109/19401736.2013.863294
Published online: 10 Jan 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: [Australian National University]
Date: 06 November 2015, At: 01:23
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 927–928 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.863294
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Esox reichertii (Amur pike) Yu Liu1,2,3 and Jun Yang1 1
Downloaded by [Australian National University] at 01:23 06 November 2015
Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, P.R. China, 2University of Chinese Academy of Sciences, Beijing, P.R. China, and 3Xiamen Environmental Protection Research Institute, Xiamen, P.R. China Abstract
Keywords
The whole mitochondrial genome of Esox reichertii (fish) was first sequenced and characterized. It was determined to be 16,909 bp long, which contains the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes. Overall base composition of the complete mitochondrial DNA was 28.65% A, 28.67% T, 27.28% C and 15.41% G, with 57.32%AT.
Esox reichertii, mitochondrial genome, protein-coding genes
This freshwater fish species (Amur pike), known as the blackspotted pike, belongs to Esociformes, Esocidae, Esox. Esox reichertii is a pike native to the Amur River system in east Asia. However, little is known about this predator. To provide the basis of genetic study, in this paper, we sequenced and annotated the whole mitochondrial genome of E. reichertii and performed similarity analysis with Esox lucius (Ishiguro et al., 2003). The samples of E. reichertii were collected from Ussuri River of the Amur River system (Heilongjiang Province, China). Total genomic DNA was extracted from alcohol-preserved caudal fin
History Received 25 October 2013 Accepted 3 November 2013 Published online 10 January 2014
tissues using the traditional phenol–chloroform method (Taggart et al., 1992). In total, 20 pairs of primers were used to amplify contiguous, overlapping segments of complete mitogenome by polymerase chain reaction (PCR). The PCR products were purified and directly sequenced by ABI 3730 DNA Sequencer (Applied Biosystems, Foster City, CA). The complete mitochondrial genome of E. reichertii is 16,909 bp (GenBank accession number: KF758446) in length including the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes (Table 1). Overall
Table 1. Mitochondrial genome organization of E. reichertii. Location Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(TAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1
Start 1 69 1011 1082 2746 2821 3799 3868 3938 4007 5058 5131 5201 5271 5305 5372 5444
Size End 69 1010 1081 2745 2820 3795 3870 3938 4006 5056 5129 5199 5273 5314 5371 5442 6994
Nucleotide (bp) 69 942 71 1664 75 975 72 71 69 1050 72 69 73 44 67 71 1551
Codon Amino acid
324
349
516
Strand H H H H H H H L H H H L L L L L H
Start
End
ATG
TAA
ATG
TAA
GTG
TAA
Intergenic nucleotide 0 0 0 0 0 0 3 3 1 0 1 1 1 3 10 0 1 (continued )
Correspondence: Jun Yang, Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, P.R. China. E-mail: [email protected]
928
Y. Liu & J. Yang
Mitochondrial DNA, 2015; 26(6): 927–928
Table 1. Continued
Location
Downloaded by [Australian National University] at 01:23 06 November 2015
Gene tRNA-Ser(AAC) tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AAG) tRNA-Leu(GCT) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro Control Region
Size
Start
End
Nucleotide (bp)
6995 7071 7150 7841 7916 8074 8756 9541 9612 9961 10,031 10,321 11,702 11,771 11,842 11,915 13,750 14,272 14,345 15,486 15,558 15,628
7065 7144 7840 7914 8083 8755 9541 9611 9961 10,030 10,327 11,701 11,770 11,839 11,914 13,753 14,271 14,342 15,481 15,558 15,627 16,909
71 74 691 74 168 682 786 71 350 70 297 1381 69 69 73 1839 522 71 1137 73 70 1282
base composition of the heavy strand was 28.65% A, 28.67% T, 27.28% C, 15.41% G, with 57.32% AT. In the CR of E. reichertii, an unusual repeat of (TATATATTAT) was detected, which is repeated 33 times. The same repeat exists in the CR of E. lucius, which is only repeated 15 times. Thus, the complete length of E. reichertii is longer than that of E. lucius. The OL is similar to most vertebrates, particularly in some fishes (Kartavtsev et al., 2007; Kim et al., 2004), between tRNA-Asn and tRNA-Cys genes. The OL, with sequence 50 -gccggggct ttcccccgctggcccctcagcgcgggggaaagtag-30 , has the potential to fold in a stem-loop secondary structure with a stem formed by 11 paired nucleotides and a loop of 12 nucleotides. The tRNA genes range in length from 67 to 75 nucleotides, which is long enough to allow the encoded tRNA to fold into its characteristic clover-leaf secondary structure. The 12S and 16S rRNA genes are 942 bp and 1664 bp long, respectively. All the mitochondrial protein-coding genes begin with an ATG start codon, except the gene for COX1, which starts with GTG. Nine genes terminated with the complete stop codons TAA (ND1, ND2, COX1, ATP8, COX3, ND4L, ND6 and Cytb) or TAG (ND5), while four other genes were inferred to have an incomplete termination codons T (COX2 ATP6, and ND4) or TA (ND3). In this study, the protein similarity of 13 pairs of homolog genes between E. reichertii and E. lucius was 99.3% (ND1), 95.1% (ND2), 99.6% (COX1), 94.3% (COX2), 87.2% (ATP8), 97.3% (ATP6), 99.2% (COX3), 99.1 (ND3), 98.9% (ND4L), 97.1% (ND4), 96.8% (ND5), 95.9% (ND6)
Codon Amino acid
230 56 227 261 116 98 460
462 173 378
Strand L H H H H H H H H H H H H H H H L L H H L H
Start
End
ATG
T
ATG ATG ATG
TAA T TAA
ATG
TA
ATG ATG
TAA T
ATG ATG
TAG TAA
ATG
TAA
Intergenic nucleotide 0 5 9 0 1 10 0 1 0 1 0 7 0 0 2 0 4 0 2 4 1 0
and 99.4% (Cytb). The whole genome sequence similarity between E. reichertii and E. lucius is 91.1%, and the gene arrangements for both species are identical.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the Scientific Support Platform for the Drinking Source Water Security in the Notrth Jiulong River. Key Projects in the Science & Technology of Xiamen City Funds (3502Z20091005).
References Ishiguro NB, Miya M, Nishida M. (2003). Basal euteleostean relationships: A mitogenomic perspective on the phylogenetic reality of the ‘Protacanthopterygii’. Mol Phylogenet Evol 27:476–88. 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 Cyt b and 16S rRNA genes. Gene 396:13–27. Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. (2004). The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–53. 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.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial genome of Esox reichertii (Amur pike) Yu Liu & Jun Yang To cite this article: Yu Liu & Jun Yang (2015) Complete mitochondrial genome of Esox reichertii (Amur pike), Mitochondrial DNA, 26:6, 927-928, DOI: 10.3109/19401736.2013.863294 To link to this article: http://dx.doi.org/10.3109/19401736.2013.863294
Published online: 10 Jan 2014.
Submit your article to this journal
Article views: 16
View related articles
View Crossmark data
Citing articles: 1 View citing articles
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Australian National University]
Date: 06 November 2015, At: 01:23
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(6): 927–928 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.863294
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Esox reichertii (Amur pike) Yu Liu1,2,3 and Jun Yang1 1
Downloaded by [Australian National University] at 01:23 06 November 2015
Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, P.R. China, 2University of Chinese Academy of Sciences, Beijing, P.R. China, and 3Xiamen Environmental Protection Research Institute, Xiamen, P.R. China Abstract
Keywords
The whole mitochondrial genome of Esox reichertii (fish) was first sequenced and characterized. It was determined to be 16,909 bp long, which contains the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes. Overall base composition of the complete mitochondrial DNA was 28.65% A, 28.67% T, 27.28% C and 15.41% G, with 57.32%AT.
Esox reichertii, mitochondrial genome, protein-coding genes
This freshwater fish species (Amur pike), known as the blackspotted pike, belongs to Esociformes, Esocidae, Esox. Esox reichertii is a pike native to the Amur River system in east Asia. However, little is known about this predator. To provide the basis of genetic study, in this paper, we sequenced and annotated the whole mitochondrial genome of E. reichertii and performed similarity analysis with Esox lucius (Ishiguro et al., 2003). The samples of E. reichertii were collected from Ussuri River of the Amur River system (Heilongjiang Province, China). Total genomic DNA was extracted from alcohol-preserved caudal fin
History Received 25 October 2013 Accepted 3 November 2013 Published online 10 January 2014
tissues using the traditional phenol–chloroform method (Taggart et al., 1992). In total, 20 pairs of primers were used to amplify contiguous, overlapping segments of complete mitogenome by polymerase chain reaction (PCR). The PCR products were purified and directly sequenced by ABI 3730 DNA Sequencer (Applied Biosystems, Foster City, CA). The complete mitochondrial genome of E. reichertii is 16,909 bp (GenBank accession number: KF758446) in length including the control region (CR), the origin of light-strand replication (OL), 22 transfer RNA genes, 2 ribosomal genes and 13 protein-coding genes (Table 1). Overall
Table 1. Mitochondrial genome organization of E. reichertii. Location Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(TAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1
Start 1 69 1011 1082 2746 2821 3799 3868 3938 4007 5058 5131 5201 5271 5305 5372 5444
Size End 69 1010 1081 2745 2820 3795 3870 3938 4006 5056 5129 5199 5273 5314 5371 5442 6994
Nucleotide (bp) 69 942 71 1664 75 975 72 71 69 1050 72 69 73 44 67 71 1551
Codon Amino acid
324
349
516
Strand H H H H H H H L H H H L L L L L H
Start
End
ATG
TAA
ATG
TAA
GTG
TAA
Intergenic nucleotide 0 0 0 0 0 0 3 3 1 0 1 1 1 3 10 0 1 (continued )
Correspondence: Jun Yang, Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, P.R. China. E-mail: [email protected]
928
Y. Liu & J. Yang
Mitochondrial DNA, 2015; 26(6): 927–928
Table 1. Continued
Location
Downloaded by [Australian National University] at 01:23 06 November 2015
Gene tRNA-Ser(AAC) tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AAG) tRNA-Leu(GCT) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro Control Region
Size
Start
End
Nucleotide (bp)
6995 7071 7150 7841 7916 8074 8756 9541 9612 9961 10,031 10,321 11,702 11,771 11,842 11,915 13,750 14,272 14,345 15,486 15,558 15,628
7065 7144 7840 7914 8083 8755 9541 9611 9961 10,030 10,327 11,701 11,770 11,839 11,914 13,753 14,271 14,342 15,481 15,558 15,627 16,909
71 74 691 74 168 682 786 71 350 70 297 1381 69 69 73 1839 522 71 1137 73 70 1282
base composition of the heavy strand was 28.65% A, 28.67% T, 27.28% C, 15.41% G, with 57.32% AT. In the CR of E. reichertii, an unusual repeat of (TATATATTAT) was detected, which is repeated 33 times. The same repeat exists in the CR of E. lucius, which is only repeated 15 times. Thus, the complete length of E. reichertii is longer than that of E. lucius. The OL is similar to most vertebrates, particularly in some fishes (Kartavtsev et al., 2007; Kim et al., 2004), between tRNA-Asn and tRNA-Cys genes. The OL, with sequence 50 -gccggggct ttcccccgctggcccctcagcgcgggggaaagtag-30 , has the potential to fold in a stem-loop secondary structure with a stem formed by 11 paired nucleotides and a loop of 12 nucleotides. The tRNA genes range in length from 67 to 75 nucleotides, which is long enough to allow the encoded tRNA to fold into its characteristic clover-leaf secondary structure. The 12S and 16S rRNA genes are 942 bp and 1664 bp long, respectively. All the mitochondrial protein-coding genes begin with an ATG start codon, except the gene for COX1, which starts with GTG. Nine genes terminated with the complete stop codons TAA (ND1, ND2, COX1, ATP8, COX3, ND4L, ND6 and Cytb) or TAG (ND5), while four other genes were inferred to have an incomplete termination codons T (COX2 ATP6, and ND4) or TA (ND3). In this study, the protein similarity of 13 pairs of homolog genes between E. reichertii and E. lucius was 99.3% (ND1), 95.1% (ND2), 99.6% (COX1), 94.3% (COX2), 87.2% (ATP8), 97.3% (ATP6), 99.2% (COX3), 99.1 (ND3), 98.9% (ND4L), 97.1% (ND4), 96.8% (ND5), 95.9% (ND6)
Codon Amino acid
230 56 227 261 116 98 460
462 173 378
Strand L H H H H H H H H H H H H H H H L L H H L H
Start
End
ATG
T
ATG ATG ATG
TAA T TAA
ATG
TA
ATG ATG
TAA T
ATG ATG
TAG TAA
ATG
TAA
Intergenic nucleotide 0 5 9 0 1 10 0 1 0 1 0 7 0 0 2 0 4 0 2 4 1 0
and 99.4% (Cytb). The whole genome sequence similarity between E. reichertii and E. lucius is 91.1%, and the gene arrangements for both species are identical.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the Scientific Support Platform for the Drinking Source Water Security in the Notrth Jiulong River. Key Projects in the Science & Technology of Xiamen City Funds (3502Z20091005).
References Ishiguro NB, Miya M, Nishida M. (2003). Basal euteleostean relationships: A mitogenomic perspective on the phylogenetic reality of the ‘Protacanthopterygii’. Mol Phylogenet Evol 27:476–88. 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 Cyt b and 16S rRNA genes. Gene 396:13–27. Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. (2004). The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–53. 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.
