http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.883607
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) Guang-Fu Hu1,2*, Xiang-Jiang Liu2*, Zhong Li1, Hong-Wei Liang1, Shao-Na Hu1, and Gui-Wei Zou1 Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, China and 2College of Fisheries, Huazhong Agricultural University, Wuhan, China
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/06/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.
Mitochondrial genome, purse red carp, Xingguo red carp
In China, numerous common carp strains have been developed in the regional distribution and cultivation zones over thousands of years. Of these, Xingguo red carp (Cyprinus carpio var. singuonensis) and Purse red carp (Cyprinus carpio var. wuyuanensis) were two traditional domestic varieties, which have been cultivated about 1300 and 800 years in Jiangxi province, China (Zhou et al., 2004). To better define the sequence variation and phylogenetic relationships within these carp varieties, we sequenced and compared the mitochondrial genome of these two varieties. The complete mitochondrial genome sequences of Xingguo red carp (JN105353) and Purse red carp (JN105357) were determined to be 16,581 bp and 16,582 bp in length, respectively. Similar to other common carp varieties (Chang et al., 1994;
History Received 6 January 2014 Accepted 12 January 2014 Published online 12 February 2014
Mabuchi et al., 2006; Wang et al., 2013), the mt-genomes of these two carp varieties all comprised of 37 genes including 13 proteincoding genes, 22 transfer RNA genes, two ribosomal RNA genes and two main non-coding regions involved in replication and transcription precesses: D-loop and the light-strand replication origin or OL (Table 1). The overall base compositions of Xingguo red carp and Purse red carp were, A: 31.90%; 31.86%, T: 24.82%; 24.81%, C: 27.53%; 27.56%, G: 15.75%; 15.77%, respectively. The overall AT and GC skew for Xingguo red carp and Purse red carp were found to be 0.125, 0.124 and 0.272, 0.272, respectively. Size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in
Table 1. Comparative analyses of mitochondrial genomes, with identity of nucleotides and predicted amino acids between purse red carp (PRC) and Xingguo red carp (XRC). Identity of nucleotides and amnio acids PRC tRNAPhe 12S rRNA tRNAVal 16S RNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2
1–69 70–1025 1026–1097 1098–2776 2777–2852 2854–3828 3833–3904 3903–3973 3976–4044 4045–5091
XRC (69) (956) (72) (1679) (76) (975) (72) (71) (69) (1047)
1–69 70–1024 1025–1096 1097–2775 2776–2851 2853–3827 3832–3903 3902–3972 3975–4043 4044–5090
bp (%) (69) (955) (72) (1679) (76) (975) (72) (71) (69) (1047)
aa (%)
Start/Stopa
Intergenic sequenceb
1 (99.9%) 1 (99.9%) 6 (99.4%)
ATG/TAA
3 (99.7%)
ATG/TAG
1 4 –2 2 2 (continued )
*These two authors contributed equally to this work. Correspondence: Gui-Wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, Wuhan East-lake Hi-tech Development Zone, Wuhan 430223, China. E-mail: [email protected]
2
G.-F. Hu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Identity of nucleotides and amnio acids
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/06/15 For personal use only.
PRC tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATPase 8 ATPase 6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop Total
5090–5160 5163–5231 5233–5305 5339–5405 5405–5475 5477–7027 7028–7098 7102–7173 7187–7877 7878–7953 7955–8119 8113–8796 8796–9581 9581–9652 9653–10,001 10,002–10,071 10,072–10,368 10,362–11,742 11,743–11,811 11,812–11,880 11,882–11,954 11,958–13,781 13,778–14,299 14,300–14,368 14,374–15,514 15,515–15,586 15,586–15,655 15,656–16,582 16,582
XRC (71) (69) (73) (67) (71) (1551) (71) (72) (691) (76) (165) (684) (786) (72) (349) (70) (297) (1381) (69) (69) (73) (1824) (522) (69) (1141) (72) (70) (927)
5089–5159 5162–5230 5232–5304 5338–5404 5404–5474 5476–7026 7027–7097 7101–7172 7186–7876 7877–7952 7954–8118 8112–8795 8795–9580 9580–9651 9652–10,000 10,001–10,070 10,071–10,367 10,361–11,741 11,742–11,810 11,811–11,879 11,881–11,953 11,957–13,780 13,777–14,298 14,299–14,367 14,373–15,513 15,514–15,585 15,585–15,654 15,655–16,581 16,581
bp (%) (71) (69) (73) (67) (71) (1551) (71) (72) (691) (76) (165) (684) (786) (72) (349) (70) (297) (1381) (69) (69) (73) (1824) (522) (69) (1141) (72) (70) (927)
aa (%)
Start/Stopa
Intergenic sequenceb 2 1 33 1 1
6 (99.7%)
GTG/TAA 3 13 ATG/T ATG/TAG ATG/TAA ATG/TAA
1 (99.9%) 1 (99.9%)
1 7 1 1
ATG/T 3 (99.8%) 1 1 6 3 1 2
(98.6%) (98.6%) (99.7%) (99.4%) (98.6) (99.8%)
1 (99.8%)
2 (99.7%)
ATG/TAA ATG/T
ATG/TAA ATG/TAA
7 1 3 4 5
ATG/T 1
3 (99.7%) 39 (99.8%)
3 (99.9%)
a
TA and T represent incomplete stop codons. Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
b
the control region, 31 in protein-coding genes. All of the proteincoding genes of the two varieties were found to use the same pattern start and stop codons (Table 1). Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 (n ¼ 2) and ND4 (n ¼ 1). The organization of 22 tRNA genes in the two varieties presented here was similar to previous published carp mitochondrial genomes. There were 3 nucleotide substitutions in 22 tRNA sequences between the two varieties, and 1 bp was located in tRNASer, 1 in tRNALeu, and 1 in tRNAGlu. Genome analysis indicated the presence of two subunits of rRNA, a 955 bp 12S rRNA and a 1679 bp 16S rRNA gene in Xingguo red carp. However, Purse red carp has a 956 bp 12S rRNA gene (Table 1). 1 bp nucleotide substitutions were observed in the 16S rRNA between the two varieties. The main control region (D-loop) in the mitochondrial genomes of the two varieties were all located between tRNAPro and tRNAPhe, and all were determined to be 927 bp long (Table 1). Comparison of the control region sequences revealed a total of three nucleotide divergences between these two varieties. Furthermore, the OL was located within a cluster of five tRNA genes (WANCY region), between tRNAAsn and tRNACys, and was 33 bp in length. This region was much conserved, and there was not any nucleotide divergence between these two strains.
Acknowledgements We would like to thank Prof. Pan Guangbi from Yangtze River Fisheries Research Institute for her help in the 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 project was supported by the earmarked fund for China Agriculture Research System (CARS-46-01) and National S&T Infrastructure Platform of China.
References Chang YC, Huang F, Lo TB. (1994). The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138–55. Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M. (2006). Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): Further evidence for an ancient origin. Aquaculture 257:68–77. Wang B, Ji P, Wang J, Sun J, Wang C, Xu P, Sun X. (2013). The complete mitochondrial genome of the Oujiang color carp, Cyprinus carpio var. color (Cypriniformes, Cyprinidae). Mitochondrial DNA 24: 19–21. Zhou J, Wu Q, Wang Z, Ye Y. (2004). Genetic variation within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Genetika 40:1389–93.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) Guang-Fu Hu1,2*, Xiang-Jiang Liu2*, Zhong Li1, Hong-Wei Liang1, Shao-Na Hu1, and Gui-Wei Zou1 Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, Wuhan, China and 2College of Fisheries, Huazhong Agricultural University, Wuhan, China
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/06/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.
Mitochondrial genome, purse red carp, Xingguo red carp
In China, numerous common carp strains have been developed in the regional distribution and cultivation zones over thousands of years. Of these, Xingguo red carp (Cyprinus carpio var. singuonensis) and Purse red carp (Cyprinus carpio var. wuyuanensis) were two traditional domestic varieties, which have been cultivated about 1300 and 800 years in Jiangxi province, China (Zhou et al., 2004). To better define the sequence variation and phylogenetic relationships within these carp varieties, we sequenced and compared the mitochondrial genome of these two varieties. The complete mitochondrial genome sequences of Xingguo red carp (JN105353) and Purse red carp (JN105357) were determined to be 16,581 bp and 16,582 bp in length, respectively. Similar to other common carp varieties (Chang et al., 1994;
History Received 6 January 2014 Accepted 12 January 2014 Published online 12 February 2014
Mabuchi et al., 2006; Wang et al., 2013), the mt-genomes of these two carp varieties all comprised of 37 genes including 13 proteincoding genes, 22 transfer RNA genes, two ribosomal RNA genes and two main non-coding regions involved in replication and transcription precesses: D-loop and the light-strand replication origin or OL (Table 1). The overall base compositions of Xingguo red carp and Purse red carp were, A: 31.90%; 31.86%, T: 24.82%; 24.81%, C: 27.53%; 27.56%, G: 15.75%; 15.77%, respectively. The overall AT and GC skew for Xingguo red carp and Purse red carp were found to be 0.125, 0.124 and 0.272, 0.272, respectively. Size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in
Table 1. Comparative analyses of mitochondrial genomes, with identity of nucleotides and predicted amino acids between purse red carp (PRC) and Xingguo red carp (XRC). Identity of nucleotides and amnio acids PRC tRNAPhe 12S rRNA tRNAVal 16S RNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2
1–69 70–1025 1026–1097 1098–2776 2777–2852 2854–3828 3833–3904 3903–3973 3976–4044 4045–5091
XRC (69) (956) (72) (1679) (76) (975) (72) (71) (69) (1047)
1–69 70–1024 1025–1096 1097–2775 2776–2851 2853–3827 3832–3903 3902–3972 3975–4043 4044–5090
bp (%) (69) (955) (72) (1679) (76) (975) (72) (71) (69) (1047)
aa (%)
Start/Stopa
Intergenic sequenceb
1 (99.9%) 1 (99.9%) 6 (99.4%)
ATG/TAA
3 (99.7%)
ATG/TAG
1 4 –2 2 2 (continued )
*These two authors contributed equally to this work. Correspondence: Gui-Wei Zou, Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences, No. 8, Wuhan East-lake Hi-tech Development Zone, Wuhan 430223, China. E-mail: [email protected]
2
G.-F. Hu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Identity of nucleotides and amnio acids
Mitochondrial DNA Downloaded from informahealthcare.com by Selcuk Universitesi on 02/06/15 For personal use only.
PRC tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer tRNAAsp COII tRNALys ATPase 8 ATPase 6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop Total
5090–5160 5163–5231 5233–5305 5339–5405 5405–5475 5477–7027 7028–7098 7102–7173 7187–7877 7878–7953 7955–8119 8113–8796 8796–9581 9581–9652 9653–10,001 10,002–10,071 10,072–10,368 10,362–11,742 11,743–11,811 11,812–11,880 11,882–11,954 11,958–13,781 13,778–14,299 14,300–14,368 14,374–15,514 15,515–15,586 15,586–15,655 15,656–16,582 16,582
XRC (71) (69) (73) (67) (71) (1551) (71) (72) (691) (76) (165) (684) (786) (72) (349) (70) (297) (1381) (69) (69) (73) (1824) (522) (69) (1141) (72) (70) (927)
5089–5159 5162–5230 5232–5304 5338–5404 5404–5474 5476–7026 7027–7097 7101–7172 7186–7876 7877–7952 7954–8118 8112–8795 8795–9580 9580–9651 9652–10,000 10,001–10,070 10,071–10,367 10,361–11,741 11,742–11,810 11,811–11,879 11,881–11,953 11,957–13,780 13,777–14,298 14,299–14,367 14,373–15,513 15,514–15,585 15,585–15,654 15,655–16,581 16,581
bp (%) (71) (69) (73) (67) (71) (1551) (71) (72) (691) (76) (165) (684) (786) (72) (349) (70) (297) (1381) (69) (69) (73) (1824) (522) (69) (1141) (72) (70) (927)
aa (%)
Start/Stopa
Intergenic sequenceb 2 1 33 1 1
6 (99.7%)
GTG/TAA 3 13 ATG/T ATG/TAG ATG/TAA ATG/TAA
1 (99.9%) 1 (99.9%)
1 7 1 1
ATG/T 3 (99.8%) 1 1 6 3 1 2
(98.6%) (98.6%) (99.7%) (99.4%) (98.6) (99.8%)
1 (99.8%)
2 (99.7%)
ATG/TAA ATG/T
ATG/TAA ATG/TAA
7 1 3 4 5
ATG/T 1
3 (99.7%) 39 (99.8%)
3 (99.9%)
a
TA and T represent incomplete stop codons. Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.
b
the control region, 31 in protein-coding genes. All of the proteincoding genes of the two varieties were found to use the same pattern start and stop codons (Table 1). Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 (n ¼ 2) and ND4 (n ¼ 1). The organization of 22 tRNA genes in the two varieties presented here was similar to previous published carp mitochondrial genomes. There were 3 nucleotide substitutions in 22 tRNA sequences between the two varieties, and 1 bp was located in tRNASer, 1 in tRNALeu, and 1 in tRNAGlu. Genome analysis indicated the presence of two subunits of rRNA, a 955 bp 12S rRNA and a 1679 bp 16S rRNA gene in Xingguo red carp. However, Purse red carp has a 956 bp 12S rRNA gene (Table 1). 1 bp nucleotide substitutions were observed in the 16S rRNA between the two varieties. The main control region (D-loop) in the mitochondrial genomes of the two varieties were all located between tRNAPro and tRNAPhe, and all were determined to be 927 bp long (Table 1). Comparison of the control region sequences revealed a total of three nucleotide divergences between these two varieties. Furthermore, the OL was located within a cluster of five tRNA genes (WANCY region), between tRNAAsn and tRNACys, and was 33 bp in length. This region was much conserved, and there was not any nucleotide divergence between these two strains.
Acknowledgements We would like to thank Prof. Pan Guangbi from Yangtze River Fisheries Research Institute for her help in the 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 project was supported by the earmarked fund for China Agriculture Research System (CARS-46-01) and National S&T Infrastructure Platform of China.
References Chang YC, Huang F, Lo TB. (1994). The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138–55. Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M. (2006). Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): Further evidence for an ancient origin. Aquaculture 257:68–77. Wang B, Ji P, Wang J, Sun J, Wang C, Xu P, Sun X. (2013). The complete mitochondrial genome of the Oujiang color carp, Cyprinus carpio var. color (Cypriniformes, Cyprinidae). Mitochondrial DNA 24: 19–21. Zhou J, Wu Q, Wang Z, Ye Y. (2004). Genetic variation within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Genetika 40:1389–93.
