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 DNA genome of tetraploid Carassius auratus gibelio Zhong Li, Hong-Wei Liang & Gui-Wei Zou To cite this article: Zhong Li, Hong-Wei Liang & Gui-Wei Zou (2014): Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.933323
Published online: 10 Sep 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: [York University Libraries]
Date: 05 November 2015, At: 23:41
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.933323
MITOGENOME ANNOUNCEMENT
Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio Zhong Li, Hong-Wei Liang, and Gui-Wei Zou
Downloaded by [York University Libraries] at 23:41 05 November 2015
Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China
Abstract
Keywords
The complete mitochondrial genome was sequenced from the tetraploid Carassius auratus gibelio in this study. The genome sequence was 16,576 bp in length. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 2 non-coding 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 31.61% A, 25.81% T, 26.62% G, 15.96% C, with an A+T bias of 57.42%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
Carassius auratus gibelio, mitochondrial genome, tetraploid
Carassius auratus gibelio is a subspecies of Carassius auratus (Rylkova´ et al, 2010), has a wide geographic distribution from northern Europe to Asia (Zhou et al., 2001). Carassius auratus gibelio has been reported co-existence of diploid, triploid and tetraploid three types of ploidy (Gui et al, 1993; Liasko et al, 2010), and the growth rate of tetraploid Carassius auratus gibelio is 38% faster than that of triploid Carassius auratus gibelio (Gui et al., 1993). In this study, one tetraploid Carassius auratus gibelio individuals was used to amplify the complete mitogenome. The complete mitogenome sequences of tetraploid Carassius auratus gibelio (KJ874431) was successfully sequenced, which was 16,576 bp in length. The mitochondrial genome of tetraploid
History Received 2 June 2014 Accepted 7 June 2014 Published online 10 September 2014
Carassius auratus gibelio comprised of 37 genes including 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (Table 1). Except for the ND6 gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, tRNAPro), all other genes were encoded on the heavy strand. The tetraploid Carassius auratus gibelio mitogenome was biased toward A+T nucleotides (57.42%). As showed in Table 1, all these protein-coding genes sequences begin with an ATG start codon except for COX1 (started with GTG codon). There were six protein-coding genes (ND1, COX1, ATPase6, COX3, ND4L, ND5) with TAA codon, three protein-coding genes (ND2, ATPase8, ND6) with TAG codon, while the other three genes (COX2, ND3, ND4, Cytb) had
Table 1. Organization of the mitochondrial genome of tetraploid Carassius auratus gibelio. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys
1 70 1024 1096 2774 2851 3830 3900 3973 4042 5087 5160 5230 5336
Size To 69 1023 1095 2773 2849 3825 3901 3970 4041 5088 5157 5228 5302 5402
Nucleotide (bp) 69 954 72 1678 76 975 72 71 69 1047 71 69 73 67
Codon Amino acid
Start
Stop
324
ATG
TAA
348
ATG
TAG
Strand
Intergenetic Nucleotide (bp)
H H H H H H H L H H H L L L
0 0 0 0 +1 +4 2 +1 0 2 +2 +1 +33 1 (continued )
Correspondence: Guiwei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, 430223, P.R. China. Tel/Fax: +8627 81780008. E-mail: [email protected]
2
Z. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Downloaded by [York University Libraries] at 23:41 05 November 2015
Tyr
tRNA COX1 tRNASer tRNAAsp COX2 tRNALys ATPase8 Atpase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop Total
Size
From
To
Nucleotide (bp)
5402 5475 7025 7099 7183 7874 7951 8109 8792 9577 9649 9998 10,068 10,358 11,739 11,808 11,878 11,954 13,774 14,296 14,370 15,511 15,582 15,653 1
5472 7025 7095 7170 7873 7949 8116 8792 9577 9648 9997 10,067 10,364 11,738 11,807 11,876 11,950 13,777 14,295 14,364 15,510 15,582 15,651 16,576 16,576
71 1551 71 72 691 76 168 684 786 72 349 70 297 1381 69 69 73 1824 522 69 1141 72 70 924 16,576
Codon Amino acid
Start
Stop
516
GTG
TAA
230
ATG
T– –
55 227 261
ATG ATG ATG
TAG TAA TAA
116
ATG
T– –
98 460
ATG ATG
TAA T– –
607 173
ATG ATG
TAA TAG
380
ATG
T– –
Strand
Intergenetic Nucleotide (bp)
L H L H H H H H H H H H H H H H H H L L H H L
+1 0 +3 +12 0 +1 7 1 1 0 0 0 7 0 0 +1 +3 4 0 +5 0 1 +1
3795
T– – represent incomplete stop codons; +Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
the incomplete stop codon T. The sequence analysis revealed that there were 22 tRNA genes in tetraploid Carassius auratus gibelio mitogenome. They were dispersed in the the genome and ranged from 69 bp to 76 bp nucleotides in size. The major non-coding sequence of the Carassius auratus gibelio mitochondrial genome is the control region (also known as D-loop), which is located between the tRNAPro and tRNAPhe genes with 924 bp in length.
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 the National Key Technology R&D Program (2012BAD26B02) and Special Basic Work Fund of Science and Technology (2013FY110700).
References Gui JF, Liang SC, Zhu LF, Jiang YG. (1993) Discovery of two different reproductive development modes of the eggs of artificial multiple tetraploid allogynogenetic silver crucian carp. Chin Sci Bull 38:332–7. Liasko R, Liousia V, Vrazeli P, Papiggioti O, Chortatou R, Abatzopoulos TJ, Leonardos ID. (2010). Biological traits of rare males in the population of Carassius gibelio (Actinopterygii: Cyprinidae) from Lake Pamvotis (north-west Greece). J Fish Biol 77:570–84. Rylkova´ K, Kalous L, Sˇlechtova´ V, Bohlen J. (2010). Many branches, one root: First evidence for a monophyly of the morphologically highly diverse goldfish (Carassius auratus). Aquaculture 302:36–41. Zhou L, Wang Y, Gui JF. (2001). Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers. Aquaculture 201:219–28.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio Zhong Li, Hong-Wei Liang & Gui-Wei Zou To cite this article: Zhong Li, Hong-Wei Liang & Gui-Wei Zou (2014): Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.933323
Published online: 10 Sep 2014.
Submit your article to this journal
Article views: 6
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: [York University Libraries]
Date: 05 November 2015, At: 23:41
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.933323
MITOGENOME ANNOUNCEMENT
Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio Zhong Li, Hong-Wei Liang, and Gui-Wei Zou
Downloaded by [York University Libraries] at 23:41 05 November 2015
Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, P.R. China
Abstract
Keywords
The complete mitochondrial genome was sequenced from the tetraploid Carassius auratus gibelio in this study. The genome sequence was 16,576 bp in length. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 2 non-coding 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 31.61% A, 25.81% T, 26.62% G, 15.96% C, with an A+T bias of 57.42%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
Carassius auratus gibelio, mitochondrial genome, tetraploid
Carassius auratus gibelio is a subspecies of Carassius auratus (Rylkova´ et al, 2010), has a wide geographic distribution from northern Europe to Asia (Zhou et al., 2001). Carassius auratus gibelio has been reported co-existence of diploid, triploid and tetraploid three types of ploidy (Gui et al, 1993; Liasko et al, 2010), and the growth rate of tetraploid Carassius auratus gibelio is 38% faster than that of triploid Carassius auratus gibelio (Gui et al., 1993). In this study, one tetraploid Carassius auratus gibelio individuals was used to amplify the complete mitogenome. The complete mitogenome sequences of tetraploid Carassius auratus gibelio (KJ874431) was successfully sequenced, which was 16,576 bp in length. The mitochondrial genome of tetraploid
History Received 2 June 2014 Accepted 7 June 2014 Published online 10 September 2014
Carassius auratus gibelio comprised of 37 genes including 13 protein coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (Table 1). Except for the ND6 gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, tRNAPro), all other genes were encoded on the heavy strand. The tetraploid Carassius auratus gibelio mitogenome was biased toward A+T nucleotides (57.42%). As showed in Table 1, all these protein-coding genes sequences begin with an ATG start codon except for COX1 (started with GTG codon). There were six protein-coding genes (ND1, COX1, ATPase6, COX3, ND4L, ND5) with TAA codon, three protein-coding genes (ND2, ATPase8, ND6) with TAG codon, while the other three genes (COX2, ND3, ND4, Cytb) had
Table 1. Organization of the mitochondrial genome of tetraploid Carassius auratus gibelio. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys
1 70 1024 1096 2774 2851 3830 3900 3973 4042 5087 5160 5230 5336
Size To 69 1023 1095 2773 2849 3825 3901 3970 4041 5088 5157 5228 5302 5402
Nucleotide (bp) 69 954 72 1678 76 975 72 71 69 1047 71 69 73 67
Codon Amino acid
Start
Stop
324
ATG
TAA
348
ATG
TAG
Strand
Intergenetic Nucleotide (bp)
H H H H H H H L H H H L L L
0 0 0 0 +1 +4 2 +1 0 2 +2 +1 +33 1 (continued )
Correspondence: Guiwei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, 430223, P.R. China. Tel/Fax: +8627 81780008. E-mail: [email protected]
2
Z. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Gene
Downloaded by [York University Libraries] at 23:41 05 November 2015
Tyr
tRNA COX1 tRNASer tRNAAsp COX2 tRNALys ATPase8 Atpase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop Total
Size
From
To
Nucleotide (bp)
5402 5475 7025 7099 7183 7874 7951 8109 8792 9577 9649 9998 10,068 10,358 11,739 11,808 11,878 11,954 13,774 14,296 14,370 15,511 15,582 15,653 1
5472 7025 7095 7170 7873 7949 8116 8792 9577 9648 9997 10,067 10,364 11,738 11,807 11,876 11,950 13,777 14,295 14,364 15,510 15,582 15,651 16,576 16,576
71 1551 71 72 691 76 168 684 786 72 349 70 297 1381 69 69 73 1824 522 69 1141 72 70 924 16,576
Codon Amino acid
Start
Stop
516
GTG
TAA
230
ATG
T– –
55 227 261
ATG ATG ATG
TAG TAA TAA
116
ATG
T– –
98 460
ATG ATG
TAA T– –
607 173
ATG ATG
TAA TAG
380
ATG
T– –
Strand
Intergenetic Nucleotide (bp)
L H L H H H H H H H H H H H H H H H L L H H L
+1 0 +3 +12 0 +1 7 1 1 0 0 0 7 0 0 +1 +3 4 0 +5 0 1 +1
3795
T– – represent incomplete stop codons; +Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
the incomplete stop codon T. The sequence analysis revealed that there were 22 tRNA genes in tetraploid Carassius auratus gibelio mitogenome. They were dispersed in the the genome and ranged from 69 bp to 76 bp nucleotides in size. The major non-coding sequence of the Carassius auratus gibelio mitochondrial genome is the control region (also known as D-loop), which is located between the tRNAPro and tRNAPhe genes with 924 bp in length.
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 the National Key Technology R&D Program (2012BAD26B02) and Special Basic Work Fund of Science and Technology (2013FY110700).
References Gui JF, Liang SC, Zhu LF, Jiang YG. (1993) Discovery of two different reproductive development modes of the eggs of artificial multiple tetraploid allogynogenetic silver crucian carp. Chin Sci Bull 38:332–7. Liasko R, Liousia V, Vrazeli P, Papiggioti O, Chortatou R, Abatzopoulos TJ, Leonardos ID. (2010). Biological traits of rare males in the population of Carassius gibelio (Actinopterygii: Cyprinidae) from Lake Pamvotis (north-west Greece). J Fish Biol 77:570–84. Rylkova´ K, Kalous L, Sˇlechtova´ V, Bohlen J. (2010). Many branches, one root: First evidence for a monophyly of the morphologically highly diverse goldfish (Carassius auratus). Aquaculture 302:36–41. Zhou L, Wang Y, Gui JF. (2001). Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers. Aquaculture 201:219–28.
