http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945545
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Paramisgurnus dabryanus Luyi Dai, Baoying Guo, Zhangjie Chu, Yong Wang, Xiaojun Wang, and Tao Huang
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
Zhejiang Ocean University, Dinghai District, Zhoushan City, P. R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of Paramisgurnus dabryanus was obtained by PCR base on 18 pairs of primers. Among the 18 primers, the 14 primers were from the previously published universal primers for Cyprinus carpio L. mitogenome amplification. The remaining 4 primers were designed on the basis of related species mtDNA sequences. The genome is 16,570 bp in length, including 2 ribosomal RNA genes. 13 proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition of Paramisgurnus dabryanus is T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence is a slight A + T bias of 55.8%, which is similar to other fishes. Mitochondrial genome is widely used in phylogenetic analysis, evolutionary genomics, species identification and related research of fish.
Mitochondrial DNA, Paramisgurnus dabryanus, sequence analysis
The Paramisgurnus dabryanus is a commercially important Cypriniformes fish species in China. Paramisgurnus dabryanus is endemic species in China, widely distributed in Sichuan, Zhejiang, Taiwan, Liaoning, Heilongjiang, etc. (Chongjie et al., 2001). The taxonomic status of different zoogeographic units is still unclear, therefore, it is very important to characterize the complete mitochondrial genome (mitogenome) of this species, which can be utilized in research on taxonomic resolution, population genetic structure and phylogeography, and phylogenetic relationship. In this study, we sequenced the complete
History Received 22 June 2014 Accepted 27 June 2014 Published online 4 August 2014
mitogenome of Paramisgurnus dabryanus with a GenBank accession number KJ027397. The total genomic DNA was extracted from back muscle tissues by Phenol–chloroform extraction (Sambrook & Russell, 2001). The voucher specimen was collected from aquaculture base, Zhoushan city, Zhejiang province, China. The complete mitochondrial genome sequences were amplified by 18 pairs of primers which were initially published Cyprinus carpio L. (Table 1). The complete mitochondrial genome was 16,570 bp in length, including 2 ribosomal RNA genes, 13 proteins-coding genes, 22 transfer RNA genes,
Table 1. PCR and sequencing primers used in this study.
PCR 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
Sequence(50 !30 ) L primers
Sequence(50 !30 ) H primers
CCAGCTAGCTAAACATTATACTAAATT CGCCTGTTTACCAAAAACAT TGAGCMTCWAATTCMAAATA CACCACCCWCGAGCAGTTGA GCAAGCCAGACACTTTAATT TATATAGGAATRGTMTGAGC GATGCCTACACMCTGTGAAA TGYGGAGCWAATCAYAGCTT AACGTTTAATGGCCCACCAAGC TTCTGAGCCTTCTAYCA TTTGAYCTAGAAATYGC GCKTTTTCKGCKTGTGAAGC AGACRTTAGATTGTGATTCTA AACACMTCTTAYCTWAACGC AACCACCGTTGTTATTCAACTA GCCTGATGAAACTTTGGCTC TTTAACTCCCACCACTGG TCCTGACTTTATCATCGGC
GCTAGGTTTAATGCTTATTTTGTAAG ATGTTGGCGTATTCKGCKAGGAA CGKAGRTAGAAGTAKAGGCT TGGGTGCCAATGTCTTTGTG GATGGATGAGTTAGCTAGAACAAT AWGGGGGTTCRATTCCTYCCTTTCTC CACCWGTTTTTGGCTTAAAAGGC CTGTGGTGAGCYCAKGT GGAKGWGGGTCASAGTCATTT CAAGACKGKGTGATTGGAAG GATTATWAGKGGGAGWAGTCA TTGCACCAAGAGTTTTTGGTTCCTAAGACC GCGATKATGCTTCCTCAGGC GGTGGCKCCTCAGAAGGACATTTGKCCTCA TAGGCRAATAGGAARTATCA GAGCCAAATGCMAGGAATARWTCA TGAGCTTCAGATGTTCAGG CTATCACCAAGTTCGGTAGGT
Correspondence: Zhangjie Chu, Zhejiang Ocean University, No.1, Rd. Southern Haida, Xingcheng New Area, Dinghai District, Zhoushan City 316022, P. R. China. E-mail: [email protected]
2
L. Dai et al.
Mitochondrial DNA, Early Online: 1–3
Table 2. Mitochondrial genome characteristics of the P. dabryanus. Position Gene
From
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(GUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro CR
Size(bp) To
Nucleotide
1 70 1023 1095 2773 2849 3829 3898 3971 4040 5085 5157 5228
69 1022 1094 2772 2847 3823 3900 3969 4039 5086 5155 5226 5300
69 953 72 1678 75 975 72 72 69 1047 71 70 73
5331 5397 5467 7019 7090 7175 7866 7943 8101 8784 9568 9641 9991 10,061 10,351 11,733 11,802 11,871 11,944 13,779 14,301 14,377 15,518 15,588 15,658
5396 5465 7017 7089 7161 7865 7941 8110 8784 9567 9640 9991 10,060 10,357 11,733 11,801 11,869 11,943 13,782 14,300 14,369 15,517 15,589 15,657 16,570
66 69 1551 71 72 691 76 168 684 784 73 351 70 297 1383 69 68 73 1839 522 69 1141 72 70 913
Codon
Amino acid
Initiation
Stop
324
ATG
TAA
348
ATG
TAA
Intergenic nucleotides
1 5 –2 1 1 1
516
GTG
TAA
1 1
230
ATG
T
13
55 227 261
ATG ATG ATG
TAA TAA T
1 –10 –1
116
ATG
TAA
98 460
ATG ATG
TAA TAG
612 173
ATG TTA
TAA CAT
–4
380
ATG
T
7
–1 –7 –1 1
and a non-coding control region (Table 2). The overall base composition of Paramisgurnus dabryanus was T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence was a slight A + T bias of 55.8%, which was similar to other fishes. Most of the protein genes used ATG as the initiation condons (ND1, ND2, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, Cytb), except for COX1 and ND6 genes, which used GTG and ATA instead of ATG. Eight protein-coding genes ended with complete termination codons, TAA (ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND5), Gene ND4 used TAG as termination codons, and ND6 use CAT instead of TAA. COX2, COX3 and Cytb shares the incomplete stop codons T. Except for eight tRNA (tRNASer, tRNAPro, tRNAGlu, tRNATyr, tRNACys, tRNAAs, tRNAAla, tRNAGln) and the ND6 genes encoded on the L-strand, the other genes were encoded on the H-strand. The 21 kinds of tRNA, tRNALeu and tRNASer repeated in the complete mitochondrial genome, respectively. According to the location of 21 tRNA, it can be divided into three tRNA clusters (IQM, WANCY, and HSL). This feature is similar to other fish mitochondrial genes. The complete mitgenome sequence of P. dabryanus had 16SRNA (1678 bp) and 12SRNA (953 bp), which were located between tRNAPhe with tRNALeu(UUR) and were separated by tRNAVal genes. The location is same with most vertebrates that has high conservative. As in most vertebrates, two non-coding regions were found in P. dabryanus mitogenome, the only CR(913 bp) gene
–2
Strand H H H H H H H L H H H L 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
located between tRNAPro and tRNAPhe, and an OL (30 bp) was located between tRNAAsn and tRNACys. The 21 tRNA genes, ranging from 66 to 76 bp in size, except for tRNASer(AGY), which lacks a dihydrouridine arm, could be folded into cloverleaf secondary structure. The origin of L-strand was in the WANCY region including five tRNA genes (tRNATrp, tRNAAla, tRNAAsn, tRNACys and tRNATyr) and it can fold into a stem-loop secondary structure with the conserved motif 50 -GCCGG-30 . There are two reading frame overlaps occur on the same strand: ATP8 and ATP6 overlap by 10 nt, and ND4L and ND4 overlap by 7 nt. The mitochondrial genome sequence of P. dabryanus submit to the GenBank (GenBank accession number: KJ027397) and were aligned by BLAST, compared with loach the sequence similarity could reach 99%. By analyzing the results, we could infer that the loach and P. dabryanus belong to the same genus.
Declaration of interest This study was supported by the Fuyang Science Bureau of China. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Avise JC. (1986). Mitochondrial DNA and evolutionary genetics of higher animals. Philos Trans R Soc Lond 312:325–42.
DOI: 10.3109/19401736.2014.945545
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
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. Chongjie C, Jiarong Z, Qixing Y. (2001). Genetic variation of two loach species revealed by RAPD analysis. J Anim 47:89–93 (in Chinese). Inoue JG, Miya M, Tsukamoto K, Nishida M. (2000). Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish Sci 66:924–32.
Mitochondrial genome of Paramisgurnus dabryanus
3
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. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring, New York: Harbor Laboratory Press.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Paramisgurnus dabryanus Luyi Dai, Baoying Guo, Zhangjie Chu, Yong Wang, Xiaojun Wang, and Tao Huang
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
Zhejiang Ocean University, Dinghai District, Zhoushan City, P. R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of Paramisgurnus dabryanus was obtained by PCR base on 18 pairs of primers. Among the 18 primers, the 14 primers were from the previously published universal primers for Cyprinus carpio L. mitogenome amplification. The remaining 4 primers were designed on the basis of related species mtDNA sequences. The genome is 16,570 bp in length, including 2 ribosomal RNA genes. 13 proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition of Paramisgurnus dabryanus is T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence is a slight A + T bias of 55.8%, which is similar to other fishes. Mitochondrial genome is widely used in phylogenetic analysis, evolutionary genomics, species identification and related research of fish.
Mitochondrial DNA, Paramisgurnus dabryanus, sequence analysis
The Paramisgurnus dabryanus is a commercially important Cypriniformes fish species in China. Paramisgurnus dabryanus is endemic species in China, widely distributed in Sichuan, Zhejiang, Taiwan, Liaoning, Heilongjiang, etc. (Chongjie et al., 2001). The taxonomic status of different zoogeographic units is still unclear, therefore, it is very important to characterize the complete mitochondrial genome (mitogenome) of this species, which can be utilized in research on taxonomic resolution, population genetic structure and phylogeography, and phylogenetic relationship. In this study, we sequenced the complete
History Received 22 June 2014 Accepted 27 June 2014 Published online 4 August 2014
mitogenome of Paramisgurnus dabryanus with a GenBank accession number KJ027397. The total genomic DNA was extracted from back muscle tissues by Phenol–chloroform extraction (Sambrook & Russell, 2001). The voucher specimen was collected from aquaculture base, Zhoushan city, Zhejiang province, China. The complete mitochondrial genome sequences were amplified by 18 pairs of primers which were initially published Cyprinus carpio L. (Table 1). The complete mitochondrial genome was 16,570 bp in length, including 2 ribosomal RNA genes, 13 proteins-coding genes, 22 transfer RNA genes,
Table 1. PCR and sequencing primers used in this study.
PCR 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
Sequence(50 !30 ) L primers
Sequence(50 !30 ) H primers
CCAGCTAGCTAAACATTATACTAAATT CGCCTGTTTACCAAAAACAT TGAGCMTCWAATTCMAAATA CACCACCCWCGAGCAGTTGA GCAAGCCAGACACTTTAATT TATATAGGAATRGTMTGAGC GATGCCTACACMCTGTGAAA TGYGGAGCWAATCAYAGCTT AACGTTTAATGGCCCACCAAGC TTCTGAGCCTTCTAYCA TTTGAYCTAGAAATYGC GCKTTTTCKGCKTGTGAAGC AGACRTTAGATTGTGATTCTA AACACMTCTTAYCTWAACGC AACCACCGTTGTTATTCAACTA GCCTGATGAAACTTTGGCTC TTTAACTCCCACCACTGG TCCTGACTTTATCATCGGC
GCTAGGTTTAATGCTTATTTTGTAAG ATGTTGGCGTATTCKGCKAGGAA CGKAGRTAGAAGTAKAGGCT TGGGTGCCAATGTCTTTGTG GATGGATGAGTTAGCTAGAACAAT AWGGGGGTTCRATTCCTYCCTTTCTC CACCWGTTTTTGGCTTAAAAGGC CTGTGGTGAGCYCAKGT GGAKGWGGGTCASAGTCATTT CAAGACKGKGTGATTGGAAG GATTATWAGKGGGAGWAGTCA TTGCACCAAGAGTTTTTGGTTCCTAAGACC GCGATKATGCTTCCTCAGGC GGTGGCKCCTCAGAAGGACATTTGKCCTCA TAGGCRAATAGGAARTATCA GAGCCAAATGCMAGGAATARWTCA TGAGCTTCAGATGTTCAGG CTATCACCAAGTTCGGTAGGT
Correspondence: Zhangjie Chu, Zhejiang Ocean University, No.1, Rd. Southern Haida, Xingcheng New Area, Dinghai District, Zhoushan City 316022, P. R. China. E-mail: [email protected]
2
L. Dai et al.
Mitochondrial DNA, Early Online: 1–3
Table 2. Mitochondrial genome characteristics of the P. dabryanus. Position Gene
From
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(GUN) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro CR
Size(bp) To
Nucleotide
1 70 1023 1095 2773 2849 3829 3898 3971 4040 5085 5157 5228
69 1022 1094 2772 2847 3823 3900 3969 4039 5086 5155 5226 5300
69 953 72 1678 75 975 72 72 69 1047 71 70 73
5331 5397 5467 7019 7090 7175 7866 7943 8101 8784 9568 9641 9991 10,061 10,351 11,733 11,802 11,871 11,944 13,779 14,301 14,377 15,518 15,588 15,658
5396 5465 7017 7089 7161 7865 7941 8110 8784 9567 9640 9991 10,060 10,357 11,733 11,801 11,869 11,943 13,782 14,300 14,369 15,517 15,589 15,657 16,570
66 69 1551 71 72 691 76 168 684 784 73 351 70 297 1383 69 68 73 1839 522 69 1141 72 70 913
Codon
Amino acid
Initiation
Stop
324
ATG
TAA
348
ATG
TAA
Intergenic nucleotides
1 5 –2 1 1 1
516
GTG
TAA
1 1
230
ATG
T
13
55 227 261
ATG ATG ATG
TAA TAA T
1 –10 –1
116
ATG
TAA
98 460
ATG ATG
TAA TAG
612 173
ATG TTA
TAA CAT
–4
380
ATG
T
7
–1 –7 –1 1
and a non-coding control region (Table 2). The overall base composition of Paramisgurnus dabryanus was T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence was a slight A + T bias of 55.8%, which was similar to other fishes. Most of the protein genes used ATG as the initiation condons (ND1, ND2, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, Cytb), except for COX1 and ND6 genes, which used GTG and ATA instead of ATG. Eight protein-coding genes ended with complete termination codons, TAA (ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND5), Gene ND4 used TAG as termination codons, and ND6 use CAT instead of TAA. COX2, COX3 and Cytb shares the incomplete stop codons T. Except for eight tRNA (tRNASer, tRNAPro, tRNAGlu, tRNATyr, tRNACys, tRNAAs, tRNAAla, tRNAGln) and the ND6 genes encoded on the L-strand, the other genes were encoded on the H-strand. The 21 kinds of tRNA, tRNALeu and tRNASer repeated in the complete mitochondrial genome, respectively. According to the location of 21 tRNA, it can be divided into three tRNA clusters (IQM, WANCY, and HSL). This feature is similar to other fish mitochondrial genes. The complete mitgenome sequence of P. dabryanus had 16SRNA (1678 bp) and 12SRNA (953 bp), which were located between tRNAPhe with tRNALeu(UUR) and were separated by tRNAVal genes. The location is same with most vertebrates that has high conservative. As in most vertebrates, two non-coding regions were found in P. dabryanus mitogenome, the only CR(913 bp) gene
–2
Strand H H H H H H H L H H H L 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
located between tRNAPro and tRNAPhe, and an OL (30 bp) was located between tRNAAsn and tRNACys. The 21 tRNA genes, ranging from 66 to 76 bp in size, except for tRNASer(AGY), which lacks a dihydrouridine arm, could be folded into cloverleaf secondary structure. The origin of L-strand was in the WANCY region including five tRNA genes (tRNATrp, tRNAAla, tRNAAsn, tRNACys and tRNATyr) and it can fold into a stem-loop secondary structure with the conserved motif 50 -GCCGG-30 . There are two reading frame overlaps occur on the same strand: ATP8 and ATP6 overlap by 10 nt, and ND4L and ND4 overlap by 7 nt. The mitochondrial genome sequence of P. dabryanus submit to the GenBank (GenBank accession number: KJ027397) and were aligned by BLAST, compared with loach the sequence similarity could reach 99%. By analyzing the results, we could infer that the loach and P. dabryanus belong to the same genus.
Declaration of interest This study was supported by the Fuyang Science Bureau of China. The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Avise JC. (1986). Mitochondrial DNA and evolutionary genetics of higher animals. Philos Trans R Soc Lond 312:325–42.
DOI: 10.3109/19401736.2014.945545
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 01/26/15 For personal use only.
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. Chongjie C, Jiarong Z, Qixing Y. (2001). Genetic variation of two loach species revealed by RAPD analysis. J Anim 47:89–93 (in Chinese). Inoue JG, Miya M, Tsukamoto K, Nishida M. (2000). Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish Sci 66:924–32.
Mitochondrial genome of Paramisgurnus dabryanus
3
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. Sambrook J, Russell DW. (2001). Molecular cloning: A laboratory manual. Cold Spring, New York: Harbor Laboratory Press.
