http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971283
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of Procypris merus Yuanhua Chen1, Ping Wu3, Dunxue Chen, Zongjun Li1, and Shi-Yu Bin2 Institute of Food and Science, Hunan Agriculture University, Changsha, Hunan, P.R. China, 2College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, P.R. China, and 3State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 12/23/14 For personal use only.
1
Abstract
Keywords
In this study, the complete mitochondrianl genome of Procypris merus was sequenced. It was determined to be 16,581 bp and included 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop). The descending order of the base composition on heavy strand was 31.91% A, 24.95% T, 27.39% C, 15.75% G, which is similar to other cyprinid fish mitochondrial genomes. All protein-coding genes had ATG as the start codon but the stop codons have three types. Night genes end with TAA or TAG, and COII, ND4, ND6 and Cytb genes terminate with an incomplete – –T. The complete mitochondrial genome may provide important DNA molecular data for further phylogenetic analyses for higher taxa of Cyprinidae.
Genome, mitochondrial, Procypris merus
The Procypris merus is the member of the family carp and it is an edible fish and breeding in rice fields. There was little known about the molecular information of P. merus, except for its distribution status and muscle nutrition component (Xiu & Qing, 2009). So, it was necessary to investigate the complete mitochondrial DNA genome sequences of P. merus. In this paper, we described the mitogenome sequence of P. merus, which was collected in the Guilin, Guangxi Province. In order to obtain the complete mitochondrial genomes of P. merus, we designed 14 pairs of primers based on the mitogenome sequences of Cyprinus carpio (KJ511883.1) and Ctenopharyngodon idellus (JQ231115.1). Using the PCR-based method (Chen et al., 2012) products were sequenced. Finally, we assembled all the sequences which unity a circular DNA molecules. The mitochondrial genome has been deposited in the GenBank with accession number KM461699. The total of the genomes is 16,581 bp, including 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 non-coding control region (D-loop; Table 1). Except for ND6 gene and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser (UCA), Glu and Pro) were encoded on the L-strand, all other genes were H-strand. All protein-coding genes had ATG as the start codon but the stop codons have three types. It is for ND1, COI, ATP6, COIII,
History Received 18 September 2014 Accepted 26 September 2014 Published online 28 October 2014
ND4L and ND5 genes were TAA, ND2, ATP8 and ND3 genes were TAG, and an incomplete one, – –T for COII, ND4, ND6 and Cytb genes. According to the research that an incomplete stop codon as a common mark for stopping protein translations was also observed in many other fish species (Kartavtsev et al., 2007; Peng et al., 2006). The base compositions were analyzed using MEGA5 (Tamura et al., 2011). The overall base composition of Procypris merus was 31.91% for A, 27.39% for C, 24.95% for T and 15.75% for G from which a slight AT bias could be easily found due to AT 56.86%4 GC 43.14% in both strands. The relative order of nucleotide composition matches with the nucleotide pattern of other cyprinids in the order: A4C4T4G (Wang et al., 2008). Of the 13 proteincoding genes, gene overlaps could be observed between four pairs of the contiguous genes, ATP8–ATP6, ATP6–COIII, ND4L–ND4 and ND5–ND6, and they overlap by five, one, seven and four nucleotides, The two ribosomal RNA genes, 12S rRNA gene (955 bp) and 16S rRNA gene (1679 bp), were located between tRNAPhe and tRNALeu(UUR) and separated by tRNAVal. All 22 tRNA between the genes and rRNA is about 70 bp. We hope that the present result will contribute for further exploration the freshwater fish and the study in mitochondrial inheritance mechanism.
Correspondence: Zongjun Li, Institute of Food and Science, Hunan Agriculture University, Changsha, Hunan 410128, P.R. China. Tel/Fax: +86 731 84261452. E-mail: [email protected] Shi-Yu Bin, College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541004, P.R. China. Tel/Fax: +86 731 84261551. E-mail: [email protected]
2
Y. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. The mitochondrial genome characteristics of the P. merus. Position Regions
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 12/23/14 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu (UUA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCA) tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu (CUA) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-Loop (CR)
Codon
From
To
Size (bp)
1 70 1025 1097 2776 2853 3832 3900 3975 4044 5089 5160 5230 5338 5404 5476 7027 7101 7186 7877 7954 8112 8795 9580 9652 10,001 10,071 10,361 11,742 11,815 11,881 11,957 13,777 14,297 14,373 15,514 15,583 15,665
69 1024 1096 2775 2851 3827 3903 3972 4043 5090 5159 5230 5304 5404 5474 7026 7097 7172 7875 7952 8118 8795 9580 9651 10,002 10,070 10,367 11,740 11,810 11,881 11,953 13,780 14,298 14,367 15,512 15,585 15,654 16,581
69 955 72 1679 74 975 70 73 69 1047 72 71 75 68 72 1596 73 73 690 74 168 684 783 72 351 69 297 1380 69 67 73 1839 522 71 1140 72 72 932
Start
Stop
ATG
TAA
ATG
TAG
GTG
TAA
ATG
– –T
ATG ATG ATG
TAG TAA TAA
ATG
TAG
ATG ATG
TAA T–T
ATG ATG
TAA – –T
ATG
– –T
Intergenic nucleotide
Stand
– 0 0 0 0 1 4 –4 2 –2 –2 0 –1 33 –1 1 0 3 13 1 1 –7 –1 –1 0 –2 0 –7 1 4 –1 3 –4 –2 5 1 –3 10
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 H L H
Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. H and L denote heavy and light strands.
Declaration of interest This study was supported by the National Natural Science Foundation of China (No. 31230076; 31472256) and the Natural Science Foundation of Hunan Province (14JJ2135). The authors report no conflicts of interest and are responsible for the content and writing of the paper.
References Chen DX, Chu WY, Liu XL, Nong XX, Li YL, Du SJ, Zhang JS. (2012). Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. Mitochondrial DNA 23:70–6. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipitidae): Genome description and
phylogenetic considerations inferred from the cytb and 16S rRNA genes. Gene 396:13–27. Peng Z, Wang J, He S. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376:290–7. Tamura K, Petertson D, Petertson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101. Xiu YS, Qing JA. (2009). Analysis on the flesh rate and the muscle nutrition component in Procypris merus. J Hydroecol 2: 154–6.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of Procypris merus Yuanhua Chen1, Ping Wu3, Dunxue Chen, Zongjun Li1, and Shi-Yu Bin2 Institute of Food and Science, Hunan Agriculture University, Changsha, Hunan, P.R. China, 2College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, P.R. China, and 3State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 12/23/14 For personal use only.
1
Abstract
Keywords
In this study, the complete mitochondrianl genome of Procypris merus was sequenced. It was determined to be 16,581 bp and included 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop). The descending order of the base composition on heavy strand was 31.91% A, 24.95% T, 27.39% C, 15.75% G, which is similar to other cyprinid fish mitochondrial genomes. All protein-coding genes had ATG as the start codon but the stop codons have three types. Night genes end with TAA or TAG, and COII, ND4, ND6 and Cytb genes terminate with an incomplete – –T. The complete mitochondrial genome may provide important DNA molecular data for further phylogenetic analyses for higher taxa of Cyprinidae.
Genome, mitochondrial, Procypris merus
The Procypris merus is the member of the family carp and it is an edible fish and breeding in rice fields. There was little known about the molecular information of P. merus, except for its distribution status and muscle nutrition component (Xiu & Qing, 2009). So, it was necessary to investigate the complete mitochondrial DNA genome sequences of P. merus. In this paper, we described the mitogenome sequence of P. merus, which was collected in the Guilin, Guangxi Province. In order to obtain the complete mitochondrial genomes of P. merus, we designed 14 pairs of primers based on the mitogenome sequences of Cyprinus carpio (KJ511883.1) and Ctenopharyngodon idellus (JQ231115.1). Using the PCR-based method (Chen et al., 2012) products were sequenced. Finally, we assembled all the sequences which unity a circular DNA molecules. The mitochondrial genome has been deposited in the GenBank with accession number KM461699. The total of the genomes is 16,581 bp, including 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 non-coding control region (D-loop; Table 1). Except for ND6 gene and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser (UCA), Glu and Pro) were encoded on the L-strand, all other genes were H-strand. All protein-coding genes had ATG as the start codon but the stop codons have three types. It is for ND1, COI, ATP6, COIII,
History Received 18 September 2014 Accepted 26 September 2014 Published online 28 October 2014
ND4L and ND5 genes were TAA, ND2, ATP8 and ND3 genes were TAG, and an incomplete one, – –T for COII, ND4, ND6 and Cytb genes. According to the research that an incomplete stop codon as a common mark for stopping protein translations was also observed in many other fish species (Kartavtsev et al., 2007; Peng et al., 2006). The base compositions were analyzed using MEGA5 (Tamura et al., 2011). The overall base composition of Procypris merus was 31.91% for A, 27.39% for C, 24.95% for T and 15.75% for G from which a slight AT bias could be easily found due to AT 56.86%4 GC 43.14% in both strands. The relative order of nucleotide composition matches with the nucleotide pattern of other cyprinids in the order: A4C4T4G (Wang et al., 2008). Of the 13 proteincoding genes, gene overlaps could be observed between four pairs of the contiguous genes, ATP8–ATP6, ATP6–COIII, ND4L–ND4 and ND5–ND6, and they overlap by five, one, seven and four nucleotides, The two ribosomal RNA genes, 12S rRNA gene (955 bp) and 16S rRNA gene (1679 bp), were located between tRNAPhe and tRNALeu(UUR) and separated by tRNAVal. All 22 tRNA between the genes and rRNA is about 70 bp. We hope that the present result will contribute for further exploration the freshwater fish and the study in mitochondrial inheritance mechanism.
Correspondence: Zongjun Li, Institute of Food and Science, Hunan Agriculture University, Changsha, Hunan 410128, P.R. China. Tel/Fax: +86 731 84261452. E-mail: [email protected] Shi-Yu Bin, College of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541004, P.R. China. Tel/Fax: +86 731 84261551. E-mail: [email protected]
2
Y. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. The mitochondrial genome characteristics of the P. merus. Position Regions
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 12/23/14 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu (UUA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCA) tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu (CUA) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-Loop (CR)
Codon
From
To
Size (bp)
1 70 1025 1097 2776 2853 3832 3900 3975 4044 5089 5160 5230 5338 5404 5476 7027 7101 7186 7877 7954 8112 8795 9580 9652 10,001 10,071 10,361 11,742 11,815 11,881 11,957 13,777 14,297 14,373 15,514 15,583 15,665
69 1024 1096 2775 2851 3827 3903 3972 4043 5090 5159 5230 5304 5404 5474 7026 7097 7172 7875 7952 8118 8795 9580 9651 10,002 10,070 10,367 11,740 11,810 11,881 11,953 13,780 14,298 14,367 15,512 15,585 15,654 16,581
69 955 72 1679 74 975 70 73 69 1047 72 71 75 68 72 1596 73 73 690 74 168 684 783 72 351 69 297 1380 69 67 73 1839 522 71 1140 72 72 932
Start
Stop
ATG
TAA
ATG
TAG
GTG
TAA
ATG
– –T
ATG ATG ATG
TAG TAA TAA
ATG
TAG
ATG ATG
TAA T–T
ATG ATG
TAA – –T
ATG
– –T
Intergenic nucleotide
Stand
– 0 0 0 0 1 4 –4 2 –2 –2 0 –1 33 –1 1 0 3 13 1 1 –7 –1 –1 0 –2 0 –7 1 4 –1 3 –4 –2 5 1 –3 10
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 H L H
Numbers correspond to the nucleotides separating different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. H and L denote heavy and light strands.
Declaration of interest This study was supported by the National Natural Science Foundation of China (No. 31230076; 31472256) and the Natural Science Foundation of Hunan Province (14JJ2135). The authors report no conflicts of interest and are responsible for the content and writing of the paper.
References Chen DX, Chu WY, Liu XL, Nong XX, Li YL, Du SJ, Zhang JS. (2012). Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences. Mitochondrial DNA 23:70–6. Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipitidae): Genome description and
phylogenetic considerations inferred from the cytb and 16S rRNA genes. Gene 396:13–27. Peng Z, Wang J, He S. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376:290–7. Tamura K, Petertson D, Petertson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101. Xiu YS, Qing JA. (2009). Analysis on the flesh rate and the muscle nutrition component in Procypris merus. J Hydroecol 2: 154–6.
