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
The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae) Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei & Gang Tao To cite this article: Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei & Gang Tao (2015) The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae), Mitochondrial DNA, 26:5, 757-758, DOI: 10.3109/19401736.2013.855737 To link to this article: http://dx.doi.org/10.3109/19401736.2013.855737
Published online: 07 Jan 2014.
Submit your article to this journal
Article views: 25
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Lethbridge]
Date: 05 November 2015, At: 22:49
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 757–758 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855737
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae) Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei and Gang Tao
Downloaded by [University of Lethbridge] at 22:49 05 November 2015
College of Animal Science and Technology, Anhui Agricultural University, Hefei, People’s Republic of China
Abstract
Keywords
Saurogobio dumerili is a cyprinid fish endemic to China. In this study, the complete mitochondrial genome of S. dumerili is reported, a circular molecule of 16,601 bp in length, with a base composition of 29.75% A, 25.71% T, 16.80% G and 27.75% C. It consists of 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region and a replication origin region (OL), with the typical pattern for vertebrates. The origin of L-strand replication (OL) in S. dumerili was located in a cluster of five tRNA genes (WANCY region) with 33 bp in length.
Mitochondrial genome, molecular systematics, Saurogobio dumerili
Saurogobio dumerili is a cyprinid fish endemic to China (Fishbase, 2013). It was distributed in the Qiantangjiang, Yangtze, Yellow and Pearl Rivers and the other water systems in China. In this study, the mitochondrial (mt) DNA sequence of the S. dumerilli (GenBank accession number KF151214) was determined. Specimen of S. dumerili was collected from the Wuwei section of the Yangtze River, Anhui Province, China. Whole genomic DNA was extracted from muscle tissue with the Axgen Genomic DNA Extraction Kit (Axgen, California). Primers were designed according to the mitochondrial genome sequence of Pseudogobio esocinus (NC_013759). All
History Received 30 August 2013 Revised 17 September 2013 Accepted 21 September 2013 Published online 7 January 2014
sequence data were analyzed and arranged to acquire the complete genome using the Lasergene software packages (DNASTAR, version 7.10). The complete mtDNA sequence of S. dumerili was a circular molecule 16,601 bp in length, with a base composition of 29.75% A, 25.71% T, 16.80% G and 27.75% C. The genome content and organization of S. dumerili follow the typical pattern for vertebrates (Boore, 1999; Brown, 2008), consisting of 13 proteincoding genes, 2 rRNAs, 22 tRNAs, 1 control region and a replication origin region (OL) (Table 1). Also, as in other vertebrates, most of the mitochondrial genes were encoded on the
Table 1. Organization of the mitochondrial genome of Saurogobio dumerili. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys
From 1 70 1031 1103 2789 2866 3845 3915 3987 4056 5102 5175 5245 5318 5351
Codons To 69 1030 1102 2788 2864 3840 3916 3985 4055 5102 5172 5243 5317 5350 5418
Size nucleotide (bp) 69 961 72 1686 76 975 72 71 69 1047 71 69 73 33 68
Amino acid
Initiation
Termination
324
ATG
TAG
348
ATG
TAA
Space (þ) overlap ()
Strand
0 0 0 0 1 4 2 1 0 1 2 1 0 0 2
H H H H H H H L H H H L L H L (continued )
Correspondence: Quan Wan, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, People’s Republic of China. Tel: +86 551 65786397. Fax: +86 575 88345007. Email: [email protected]
758
Q. Wan et al.
Mitochondrial DNA, 2015; 26(5): 757–758
Table 1. Continued.
Position Locus
Downloaded by [University of Lethbridge] at 22:49 05 November 2015
Tyr
tRNA COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Codons
From
To
Size nucleotide (bp)
5421 5490 7041 7115 7198 7889 7966 8124 8807 9591 9663 10,012 10,082 10,372 11,754 11,823 11,891 11,964 13,796 14,318 14,391 15,532 15,604 15,674
5488 7040 7111 7185 7888 7964 8130 8807 9590 9662 10,013 10,081 10,378 11,754 11,822 11,891 11,963 13,799 14,317 14,386 15,531 15,604 15,673 16,601
68 1551 71 71 691 76 165 684 784 72 351 70 297 1383 69 69 73 1836 522 69 1141 73 70 928
Amino acid
Initiation
Termination
516
GTG
TAA
230
ATG
T
54 227 261
ATG ATG ATG
TAA TAA T
116
ATG
TAG
98 460
ATG ATG
TAA TAG
611 173
ATG ATG
TAG TAG
380
ATG
T
H-strand, while the ND6 gene and eight tRNA genes (tRNAGln, tRNAAsn, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, tRNAPro) were encoded on the L-strand (Table 1). The mtDNA genome of S. dumerili included 10 genes overlaps, ranging from 1 to 7 bp (27 bp in total). There were 32 bp present in 11 intergenic regions, excluding the A þ T-rich region (the putative control region). All of the protein-coding genes were found to contain a canonical ATG start codon, except ND6 which appeared to employ a GTG codon (Table 1). In regard to termination codons, S. dumerili had most genes ending with complete termination codons TAA (ND2, COX I, ATP8, ATP6, ND4L) and TAG (ND1, ND3, ND4, ND5, ND6), while the COX II, COX III and Cyt b use the incomplete termination codon T (Table 1). As in other bony fish mitogenome sequences, two rRNAs genes in S. dumerili were located in the conserved position between tRNAPhe and tRNAVal, and between tRNAVal and tRNALeu(UUR). The 12S rRNA and 16S rRNA in S. dumerili were 961 and 1686 bp long, respectively (Table 1).
Space (þ) overlap () 1 0 3 12 0 1 7 1 0 0 2 0 7 1 0 1 0 4 0 4 0 1 0
Strand L H L H H H H H H H H H H H H H H H L L H H L –
The major non-coding sequence (control region) of mtDNA from S. dumerili was located between the tRNAPro and tRNAPhe genes and was 928 bp in length. The S. dumerili CR had a high A þ T content of 67.02% (A ¼ 0.3394, T ¼ 0.3308, C ¼ 0.1929, G ¼ 0.1369). The origin of L-strand replication (OL) in S. dumerili was located between the tRNAAsn and tRNACys genes within a cluster of five tRNA genes (WANCY region), which is 33 bp long (Table 1).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Brown KH. (2008). Fish mitochondrial genomics: Sequence, inheritance and functional variation. J Fish Biol 72:355–74. Fishbase. (2013). Saurogobio dumerili. [Online] Available at: http:// www.fishbase.org (Accessed 7 July 2013)
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae) Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei & Gang Tao To cite this article: Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei & Gang Tao (2015) The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae), Mitochondrial DNA, 26:5, 757-758, DOI: 10.3109/19401736.2013.855737 To link to this article: http://dx.doi.org/10.3109/19401736.2013.855737
Published online: 07 Jan 2014.
Submit your article to this journal
Article views: 25
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of Lethbridge]
Date: 05 November 2015, At: 22:49
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 757–758 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855737
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Saurogobio dumerili (Cypriniformes: Cyprinidae) Quan Wan, Zhaohui Ma, Dongdong Pan, Min Wei and Gang Tao
Downloaded by [University of Lethbridge] at 22:49 05 November 2015
College of Animal Science and Technology, Anhui Agricultural University, Hefei, People’s Republic of China
Abstract
Keywords
Saurogobio dumerili is a cyprinid fish endemic to China. In this study, the complete mitochondrial genome of S. dumerili is reported, a circular molecule of 16,601 bp in length, with a base composition of 29.75% A, 25.71% T, 16.80% G and 27.75% C. It consists of 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region and a replication origin region (OL), with the typical pattern for vertebrates. The origin of L-strand replication (OL) in S. dumerili was located in a cluster of five tRNA genes (WANCY region) with 33 bp in length.
Mitochondrial genome, molecular systematics, Saurogobio dumerili
Saurogobio dumerili is a cyprinid fish endemic to China (Fishbase, 2013). It was distributed in the Qiantangjiang, Yangtze, Yellow and Pearl Rivers and the other water systems in China. In this study, the mitochondrial (mt) DNA sequence of the S. dumerilli (GenBank accession number KF151214) was determined. Specimen of S. dumerili was collected from the Wuwei section of the Yangtze River, Anhui Province, China. Whole genomic DNA was extracted from muscle tissue with the Axgen Genomic DNA Extraction Kit (Axgen, California). Primers were designed according to the mitochondrial genome sequence of Pseudogobio esocinus (NC_013759). All
History Received 30 August 2013 Revised 17 September 2013 Accepted 21 September 2013 Published online 7 January 2014
sequence data were analyzed and arranged to acquire the complete genome using the Lasergene software packages (DNASTAR, version 7.10). The complete mtDNA sequence of S. dumerili was a circular molecule 16,601 bp in length, with a base composition of 29.75% A, 25.71% T, 16.80% G and 27.75% C. The genome content and organization of S. dumerili follow the typical pattern for vertebrates (Boore, 1999; Brown, 2008), consisting of 13 proteincoding genes, 2 rRNAs, 22 tRNAs, 1 control region and a replication origin region (OL) (Table 1). Also, as in other vertebrates, most of the mitochondrial genes were encoded on the
Table 1. Organization of the mitochondrial genome of Saurogobio dumerili. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys
From 1 70 1031 1103 2789 2866 3845 3915 3987 4056 5102 5175 5245 5318 5351
Codons To 69 1030 1102 2788 2864 3840 3916 3985 4055 5102 5172 5243 5317 5350 5418
Size nucleotide (bp) 69 961 72 1686 76 975 72 71 69 1047 71 69 73 33 68
Amino acid
Initiation
Termination
324
ATG
TAG
348
ATG
TAA
Space (þ) overlap ()
Strand
0 0 0 0 1 4 2 1 0 1 2 1 0 0 2
H H H H H H H L H H H L L H L (continued )
Correspondence: Quan Wan, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, People’s Republic of China. Tel: +86 551 65786397. Fax: +86 575 88345007. Email: [email protected]
758
Q. Wan et al.
Mitochondrial DNA, 2015; 26(5): 757–758
Table 1. Continued.
Position Locus
Downloaded by [University of Lethbridge] at 22:49 05 November 2015
Tyr
tRNA COX I tRNASer(UCN) tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control region
Codons
From
To
Size nucleotide (bp)
5421 5490 7041 7115 7198 7889 7966 8124 8807 9591 9663 10,012 10,082 10,372 11,754 11,823 11,891 11,964 13,796 14,318 14,391 15,532 15,604 15,674
5488 7040 7111 7185 7888 7964 8130 8807 9590 9662 10,013 10,081 10,378 11,754 11,822 11,891 11,963 13,799 14,317 14,386 15,531 15,604 15,673 16,601
68 1551 71 71 691 76 165 684 784 72 351 70 297 1383 69 69 73 1836 522 69 1141 73 70 928
Amino acid
Initiation
Termination
516
GTG
TAA
230
ATG
T
54 227 261
ATG ATG ATG
TAA TAA T
116
ATG
TAG
98 460
ATG ATG
TAA TAG
611 173
ATG ATG
TAG TAG
380
ATG
T
H-strand, while the ND6 gene and eight tRNA genes (tRNAGln, tRNAAsn, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu, tRNAPro) were encoded on the L-strand (Table 1). The mtDNA genome of S. dumerili included 10 genes overlaps, ranging from 1 to 7 bp (27 bp in total). There were 32 bp present in 11 intergenic regions, excluding the A þ T-rich region (the putative control region). All of the protein-coding genes were found to contain a canonical ATG start codon, except ND6 which appeared to employ a GTG codon (Table 1). In regard to termination codons, S. dumerili had most genes ending with complete termination codons TAA (ND2, COX I, ATP8, ATP6, ND4L) and TAG (ND1, ND3, ND4, ND5, ND6), while the COX II, COX III and Cyt b use the incomplete termination codon T (Table 1). As in other bony fish mitogenome sequences, two rRNAs genes in S. dumerili were located in the conserved position between tRNAPhe and tRNAVal, and between tRNAVal and tRNALeu(UUR). The 12S rRNA and 16S rRNA in S. dumerili were 961 and 1686 bp long, respectively (Table 1).
Space (þ) overlap () 1 0 3 12 0 1 7 1 0 0 2 0 7 1 0 1 0 4 0 4 0 1 0
Strand L H L H H H H H H H H H H H H H H H L L H H L –
The major non-coding sequence (control region) of mtDNA from S. dumerili was located between the tRNAPro and tRNAPhe genes and was 928 bp in length. The S. dumerili CR had a high A þ T content of 67.02% (A ¼ 0.3394, T ¼ 0.3308, C ¼ 0.1929, G ¼ 0.1369). The origin of L-strand replication (OL) in S. dumerili was located between the tRNAAsn and tRNACys genes within a cluster of five tRNA genes (WANCY region), which is 33 bp long (Table 1).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Brown KH. (2008). Fish mitochondrial genomics: Sequence, inheritance and functional variation. J Fish Biol 72:355–74. Fishbase. (2013). Saurogobio dumerili. [Online] Available at: http:// www.fishbase.org (Accessed 7 July 2013)
