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
Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) Heng Wang, Xieqiang Wu, Qingjj Lv, Shiping Su, Gaopeng Li, Yuru Lin, Yi Lu & Yiping Meng To cite this article: Heng Wang, Xieqiang Wu, Qingjj Lv, Shiping Su, Gaopeng Li, Yuru Lin, Yi Lu & Yiping Meng (2014): Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.987247
Published online: 09 Dec 2014.
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Date: 05 November 2015, At: 22:39
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987247
MITOGENOME ANNOUNCEMENT
Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) Heng Wang1,2, Xieqiang Wu1, Qingjj Lv1, Shiping Su1, Gaopeng Li2, Yuru Lin2, Yi Lu2, and Yiping Meng2 College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China and 2College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Mitochondrial DNA
1
Abstract
Keywords
The total mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) is 16,612 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The overall nucleotide composition of the H-strand of H. labeo mitochondrial genome is A: 29.82%, G: 17.11%, T: 25.90% and C: 27.17%, respectively, with an A + T-rich feature (55.72%). These results will contribute to the natural resources conservation and species identification of H.labeo.
Hemibarbus labeo, mitochondrial genome, sequencing
The Hemibarbus labeo (Cypriniformes:Cyprinidae) is a small fish distributed widely in China. In this study, the complete mitochondrial genome was sequenced from an individual of H. labeo (designated SU-PO2014). Comparison of mitochondrial genome information has proved to be a powerful tool for resolving phylogenetic relationships at various taxonomic levels of each species (Chen et al., 2013; Min & Park, 2009; Yang et al., 2013). The complete mitochondrial genome sequence of H. labeo (GenBank accession no. KP064328) was determined to be 16,612 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region. The overall nucleotide composition of the H-strand of H. labeo mitochondrial genome is A: 29.82%, G: 27.11%, T: 25.90% and C: 27.17%.
History Received 2 November 2014 Accepted 10 November 2014 Published online 9 December 2014
All genes were encoded on the heavy strand (H-strand), with the exception of eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu and tRNAPro) and one protein-coding gene (ND6). All the genes showed typical gene arrangement conforming to the vertebrate consensus (Wang et al., 2013; Yang et al., 2013) (Table 1). The remaining protein-coding genes initiate with ATG start codon except for COX I with a GTG. Regarding stop codons, seven protein-coding genes end with TAA (ND1, ND2, COX I, ATP8, ATP6, ND4L and ND6), whereas the genes ND4 and ND5 terminate with TAG. Incomplete stop codons are found in COX III (TA–), as well as and ND3 and COX II and Cyt b (T– –), respectively. After the pairwise analysis, the complete mitogenome sites having 109 variable sites (105 base substitutions and 4 indels)
Table 1. Organization of the mitochondrial genome of H. labeo. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet
Abbreviations F 12S V 16S L nd1 I Q M
From 1 70 1029 1101 2793 2870 3849 3919 3991
To 69 1028 1100 2792 2868 3844 3920 3989 4059
Codon Size of nucleotide (bp) 69 959 72 1692 76 975 72 71 69
Start
Stop
Amino acid Anti-codon Intergenic nucleotide Strand GAA TAC TAA
ATG TAA
324 GAT TTG CAT
0 0 0 0 1 4 2 1 0
H H H H H H H L H (continued )
Correspondence: Shiping Su, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, P.R.China. Tel/Fax: 86 551 65789397. E-mail: [email protected]
2
H. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position
Mitochondrial DNA
Locus ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr 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
Codon
Abbreviations
From
To
Size of nucleotide (bp)
nd2 W A N
4060 5105 5178 5248 5321 5353 5422 5494 7046 7119 7204 7895 7972 8130 8813 9597 9670 10,019 10,089 10,379 11,761 11,830 11,900 11,973 13,805 14,327 14,400 15,541 15,613 15,681
5106 5175 5246 5320 5352 5420 5492 7044 7114 7190 7894 7970 8136 8813 9597 9669 10,018 10,088 10,385 11,761 11,829 11,898 11,972 13,808 14,326 14,395 15,540 15,612 15,680 16,612
1047 71 69 73 32 68 71 1551 69 72 691 76 165 684 785 73 349 70 297 1383 69 69 73 1836 522 69 1141 72 68 932
C Y cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
were determined between H. labeo (SU-PO2013) and H. labeo (SU-PO2014), accounting for 0.66% of the complete mitogenome sites, these base substitutions were distributed in all protein-coding genes, one tRNA genes (tRNALeu) and a non-coding region (D-loop). Among them, four proteincoding genes (ND1, ND2, ND4 and ND5) have relatively higher variable sites with 13, 11, 16 and 13 variable sites, respectively. All indels were only detected in 16SrRNA, which have eight variable sites.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the grand of 2014XKPY and NO. KJ03090304.
Start
Stop
ATG TAG
Amino acid Anti-codon Intergenic nucleotide Strand 348 TCA TGC GTT GCA GTA
GTG TAA
516 TGA GTC
ATG
T– –
230
ATG TAA ATG TAA ATG TA–
54 227 261
ATG
T– –
116
ATG TAA ATG TAG
98 460
TTT
TCC TCG GTG TAG ATG TAA ATG TAG
611 173
ATG
380
TTC T– –
TGT TGG
2 2 1 0 0 1 1 1 4 13 0 1 7 1 1 0 0 0 7 1 0 1 0 4 0 4 0 0 0
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 -
References Chen X, Zhou ZM, Chen ZJ, Ai WM. (2013). Complete mitochondrial genome of Sarcocheilichthys parvus (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:97–8. Min GS, Park JK. (2009). Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata). BMC Genomics 10:533. Wang H, He L, Yang X, Yang S, Li C, Wang X. (2014). Determination of the complete mitochondrial genome sequence of mussel Cristaria plicata (Leach). Mitochondrial DNA [Epub ahead of print]. DOI:10.3109/19401736.2014.953100. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA 25: 286–7.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) Heng Wang, Xieqiang Wu, Qingjj Lv, Shiping Su, Gaopeng Li, Yuru Lin, Yi Lu & Yiping Meng To cite this article: Heng Wang, Xieqiang Wu, Qingjj Lv, Shiping Su, Gaopeng Li, Yuru Lin, Yi Lu & Yiping Meng (2014): Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.987247
Published online: 09 Dec 2014.
Submit your article to this journal
Article views: 7
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: [Texas A & M International University]
Date: 05 November 2015, At: 22:39
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987247
MITOGENOME ANNOUNCEMENT
Identification and description of the mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) Heng Wang1,2, Xieqiang Wu1, Qingjj Lv1, Shiping Su1, Gaopeng Li2, Yuru Lin2, Yi Lu2, and Yiping Meng2 College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China and 2College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Mitochondrial DNA
1
Abstract
Keywords
The total mitochondrial genome of Hemibarbus labeo (Cypriniformes: Cyprinidae) is 16,612 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The overall nucleotide composition of the H-strand of H. labeo mitochondrial genome is A: 29.82%, G: 17.11%, T: 25.90% and C: 27.17%, respectively, with an A + T-rich feature (55.72%). These results will contribute to the natural resources conservation and species identification of H.labeo.
Hemibarbus labeo, mitochondrial genome, sequencing
The Hemibarbus labeo (Cypriniformes:Cyprinidae) is a small fish distributed widely in China. In this study, the complete mitochondrial genome was sequenced from an individual of H. labeo (designated SU-PO2014). Comparison of mitochondrial genome information has proved to be a powerful tool for resolving phylogenetic relationships at various taxonomic levels of each species (Chen et al., 2013; Min & Park, 2009; Yang et al., 2013). The complete mitochondrial genome sequence of H. labeo (GenBank accession no. KP064328) was determined to be 16,612 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region. The overall nucleotide composition of the H-strand of H. labeo mitochondrial genome is A: 29.82%, G: 27.11%, T: 25.90% and C: 27.17%.
History Received 2 November 2014 Accepted 10 November 2014 Published online 9 December 2014
All genes were encoded on the heavy strand (H-strand), with the exception of eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(UCN), tRNAGlu and tRNAPro) and one protein-coding gene (ND6). All the genes showed typical gene arrangement conforming to the vertebrate consensus (Wang et al., 2013; Yang et al., 2013) (Table 1). The remaining protein-coding genes initiate with ATG start codon except for COX I with a GTG. Regarding stop codons, seven protein-coding genes end with TAA (ND1, ND2, COX I, ATP8, ATP6, ND4L and ND6), whereas the genes ND4 and ND5 terminate with TAG. Incomplete stop codons are found in COX III (TA–), as well as and ND3 and COX II and Cyt b (T– –), respectively. After the pairwise analysis, the complete mitogenome sites having 109 variable sites (105 base substitutions and 4 indels)
Table 1. Organization of the mitochondrial genome of H. labeo. Position Locus Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet
Abbreviations F 12S V 16S L nd1 I Q M
From 1 70 1029 1101 2793 2870 3849 3919 3991
To 69 1028 1100 2792 2868 3844 3920 3989 4059
Codon Size of nucleotide (bp) 69 959 72 1692 76 975 72 71 69
Start
Stop
Amino acid Anti-codon Intergenic nucleotide Strand GAA TAC TAA
ATG TAA
324 GAT TTG CAT
0 0 0 0 1 4 2 1 0
H H H H H H H L H (continued )
Correspondence: Shiping Su, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, P.R.China. Tel/Fax: 86 551 65789397. E-mail: [email protected]
2
H. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position
Mitochondrial DNA
Locus ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr 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
Codon
Abbreviations
From
To
Size of nucleotide (bp)
nd2 W A N
4060 5105 5178 5248 5321 5353 5422 5494 7046 7119 7204 7895 7972 8130 8813 9597 9670 10,019 10,089 10,379 11,761 11,830 11,900 11,973 13,805 14,327 14,400 15,541 15,613 15,681
5106 5175 5246 5320 5352 5420 5492 7044 7114 7190 7894 7970 8136 8813 9597 9669 10,018 10,088 10,385 11,761 11,829 11,898 11,972 13,808 14,326 14,395 15,540 15,612 15,680 16,612
1047 71 69 73 32 68 71 1551 69 72 691 76 165 684 785 73 349 70 297 1383 69 69 73 1836 522 69 1141 72 68 932
C Y cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
were determined between H. labeo (SU-PO2013) and H. labeo (SU-PO2014), accounting for 0.66% of the complete mitogenome sites, these base substitutions were distributed in all protein-coding genes, one tRNA genes (tRNALeu) and a non-coding region (D-loop). Among them, four proteincoding genes (ND1, ND2, ND4 and ND5) have relatively higher variable sites with 13, 11, 16 and 13 variable sites, respectively. All indels were only detected in 16SrRNA, which have eight variable sites.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was supported by the grand of 2014XKPY and NO. KJ03090304.
Start
Stop
ATG TAG
Amino acid Anti-codon Intergenic nucleotide Strand 348 TCA TGC GTT GCA GTA
GTG TAA
516 TGA GTC
ATG
T– –
230
ATG TAA ATG TAA ATG TA–
54 227 261
ATG
T– –
116
ATG TAA ATG TAG
98 460
TTT
TCC TCG GTG TAG ATG TAA ATG TAG
611 173
ATG
380
TTC T– –
TGT TGG
2 2 1 0 0 1 1 1 4 13 0 1 7 1 1 0 0 0 7 1 0 1 0 4 0 4 0 0 0
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 -
References Chen X, Zhou ZM, Chen ZJ, Ai WM. (2013). Complete mitochondrial genome of Sarcocheilichthys parvus (Cypriniformes, Cyprinidae). Mitochondrial DNA 24:97–8. Min GS, Park JK. (2009). Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata). BMC Genomics 10:533. Wang H, He L, Yang X, Yang S, Li C, Wang X. (2014). Determination of the complete mitochondrial genome sequence of mussel Cristaria plicata (Leach). Mitochondrial DNA [Epub ahead of print]. DOI:10.3109/19401736.2014.953100. Yang SB, Wei M, Wan Q, He LP, Wang H, Tao G, Han JW, Li C. (2013). The complete mitochondrial genome sequence of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae). Mitochondrial DNA 25: 286–7.
