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
The complete mitochondrial genome of Andinoacara rivulatus Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai & Xiaolian Liu To cite this article: Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai & Xiaolian Liu (2014): The complete mitochondrial genome of Andinoacara rivulatus, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.987268
Published online: 10 Dec 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: [Australian National University]
Date: 06 November 2015, At: 07:23
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987268
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Andinoacara rivulatus Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai, and Xiaolian Liu
Downloaded by [Australian National University] at 07:23 06 November 2015
Aquaculture Technology Research Laboratory, Tianjin Fisheries Research Institute, Tianjin, People’s Republic of China
Abstract
Keywords
The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Andinoacara rivulatus from Lizigu farm, Tianjin city, China. The mitogenome was determined to be 16,585 bp in length. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The sequence structure of non-coding control region was also analyzed. This is the first report on the complete mitogenome sequence of A. rivulatus.
Andinoacara rivulatus, mitochondrial genome, polymerase chain reaction
Andinoacara rivulatus belongs to the Andinoacara genus, Cichlidae family, which was originated from western Ecuador and Peru. It is one of the most popular cichlids in the aquarium fish trade due to its striking colors and impressive appearance. In this study, the complete mitochondrial genome of A. rivulatus from Lizigu farm, Tianjin city was determined. Total genomic DNA was extracted using the DNeasy Tissue Kit (Qiagen, Valencia, CA). The complete mitochondrial genome of A. Rivulatus was amplified by traditional polymerase chain reaction method and sequenced using Sanger’s method. The mitochondrial DNA sequences were then assembled as described in the previous studies (Li et al., 2014; Xue et al., 2013). We annotated the complete genome sequence using MitoAnnotator (Iwasaki et al., 2013). The complete mitochondrial genome of A. rivulatus was 16,585 bp in length (DDBJ accession number: LC009435) with a typical mitogenome structure of 13 protein-coding genes (PCGs),
History Received 10 November 2014 Accepted 10 November 2014 Published online 10 December 2014
22 tRNA genes, 2 rRNA genes and a control region (Table 1). The average base composition of the novel mitogenome is 27.88% for A, 28.98% for T, 27.15% for C and 15.99% for G. The control region D-loop is located between tRNAPro and tRNAPhe with 846 bp in size. The 12S rRNA and 16S rRNA were interspersed between the tRNAPhe and tRNALeu and separated by the tRNAVal. They were 946 and 1695 bp in size, respectively. Twelve PCGs, 14 tRNAs and 2 rRNAs were encoded on the H-strand and the remaining genes were on the L-strand. A total of four overlaps among PCGs and tRNAs were identified in this genome. The start codons of all PCGs are ATG, except COI (GTG). Four PCGs used TAA (ND1, ATPase8, ND4L, Cytb) as the stop codons and 3 PCGs used TAG (COI, ND5 and ND6) as the stop codons. The rest PCGs ended with the incomplete stop codon T (COII, COIII, ND2, ND3 and ND4) or TA (ATPase6). Twenty-two tRNAs were located among the rRNAs and PCGs. The central conserved sequences of CSB-F, CSB-E and CSB-D were determined in the
Table 1. Characteristics of the mitochondrial genome of A. rivulatus. Location Locus Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UAA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Start 1 70 1016 1088 2783 2857 3835 3904 3974 4043 5088
Codon Stop 69 1015 1087 2782 2856 3831 3904 3974 4042 5087 5159
Size of nucleotide (bp) 69 946 72 1695 74 975 70 71 69 1045 72
Amino acid
Start
Stop
324
ATG
TAA
348
ATG
T– –
Intergenic nucleotide* 0 0 0 0 0 3 1 1 0 0
Strand H H H H H H H L H H H (continued )
Correspondence: Zhijing Sun, Aquaculture Technology Research Laboratory, Tianjin Fisheries Research Institute, Tianjin 300221, People’s Republic of China. Tel: +86-22-88250594. Fax: +86-22-88252084. E-mail: [email protected]
2
C. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Location Locus
Downloaded by [Australian National University] at 07:23 06 November 2015
Ala
tRNA tRNAAsn tRNACys tRNATyr COI tRNASer(UGA) tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(GCU) tRNALeu(UAG) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Codon
Start
Stop
Size of nucleotide (bp)
5161 5231 5340 5406 5477 7116 7189 7266 7957 8031 8189 8872 9656 9727 10,073 10,142 10,432 11,813 11,882 11,953 12,026 13,873 14,383 14,456 15,597 15,671 15,740
5229 5303 5405 5475 7039 7186 7261 7956 8029 8198 8871 9655 9726 10,072 10,141 10,438 11,812 11,881 11,948 12,025 13,864 14,382 14,451 15,592 15,668 15,739 16,585
69 73 66 70 1563 71 73 691 73 168 683 784 71 346 69 297 1381 69 67 73 1839 510 69 1137 72 69 846
Amino acid
Start
Stop
520
GTG
TAG
230
ATG
T– –
55 227 261
ATG ATG ATG
TAA TA– T– –
116
ATG
T– –
98 460
ATG ATG
TAA T– –
612 173
ATG ATG
TAG TAG
378
ATG
TAA
Intergenic nucleotide* 1 1 36 0 1 76 2 4 0 1 10 0 0 0 0 0 7 0 0 4 0 8 0 4 4 2 0
Strand 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 and L indicate heavy and light strands. *Numbers correspond to the nucleotides separating different genes, negative numbers represent the overlapping nucleotides.
positions 16,105–16,033, 16,065–16,091 and 16,106–16,128 bp. The conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were in the positions 16,377–16,398, 16,452–16,477 and 16,499– 16,524 bp, respectively.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We acknowledge grant support from the Tianjin science and technology plan projects (12ZCZDNC01100, 14ZXNZNC00046) and Research Program of Application Foundation and Advanced Technology of Tianjin (11JCYBJC08800).
References Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Li CY, Li JT, Xiao GB, Hou GY, Sun XW. (2014). Complete mitochondrial genome of the kissing gourami, Helostoma temminkii. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736. 2013.861451. Xue W, Hou GY, Li CY, Kong XF, Zheng XH, Li JT, Sun XW. (2013). Complete mitochondrial genome of Chinese sleeper, Perccottus glenii. Mitochondrial DNA 24:339–41.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Andinoacara rivulatus Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai & Xiaolian Liu To cite this article: Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai & Xiaolian Liu (2014): The complete mitochondrial genome of Andinoacara rivulatus, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.987268
Published online: 10 Dec 2014.
Submit your article to this journal
Article views: 18
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: [Australian National University]
Date: 06 November 2015, At: 07:23
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987268
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Andinoacara rivulatus Chunyan Li, Zhijing Sun, Shouming Feng, Jufeng Jiang, Huimin Wu, Xiaohui Bai, and Xiaolian Liu
Downloaded by [Australian National University] at 07:23 06 November 2015
Aquaculture Technology Research Laboratory, Tianjin Fisheries Research Institute, Tianjin, People’s Republic of China
Abstract
Keywords
The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Andinoacara rivulatus from Lizigu farm, Tianjin city, China. The mitogenome was determined to be 16,585 bp in length. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The sequence structure of non-coding control region was also analyzed. This is the first report on the complete mitogenome sequence of A. rivulatus.
Andinoacara rivulatus, mitochondrial genome, polymerase chain reaction
Andinoacara rivulatus belongs to the Andinoacara genus, Cichlidae family, which was originated from western Ecuador and Peru. It is one of the most popular cichlids in the aquarium fish trade due to its striking colors and impressive appearance. In this study, the complete mitochondrial genome of A. rivulatus from Lizigu farm, Tianjin city was determined. Total genomic DNA was extracted using the DNeasy Tissue Kit (Qiagen, Valencia, CA). The complete mitochondrial genome of A. Rivulatus was amplified by traditional polymerase chain reaction method and sequenced using Sanger’s method. The mitochondrial DNA sequences were then assembled as described in the previous studies (Li et al., 2014; Xue et al., 2013). We annotated the complete genome sequence using MitoAnnotator (Iwasaki et al., 2013). The complete mitochondrial genome of A. rivulatus was 16,585 bp in length (DDBJ accession number: LC009435) with a typical mitogenome structure of 13 protein-coding genes (PCGs),
History Received 10 November 2014 Accepted 10 November 2014 Published online 10 December 2014
22 tRNA genes, 2 rRNA genes and a control region (Table 1). The average base composition of the novel mitogenome is 27.88% for A, 28.98% for T, 27.15% for C and 15.99% for G. The control region D-loop is located between tRNAPro and tRNAPhe with 846 bp in size. The 12S rRNA and 16S rRNA were interspersed between the tRNAPhe and tRNALeu and separated by the tRNAVal. They were 946 and 1695 bp in size, respectively. Twelve PCGs, 14 tRNAs and 2 rRNAs were encoded on the H-strand and the remaining genes were on the L-strand. A total of four overlaps among PCGs and tRNAs were identified in this genome. The start codons of all PCGs are ATG, except COI (GTG). Four PCGs used TAA (ND1, ATPase8, ND4L, Cytb) as the stop codons and 3 PCGs used TAG (COI, ND5 and ND6) as the stop codons. The rest PCGs ended with the incomplete stop codon T (COII, COIII, ND2, ND3 and ND4) or TA (ATPase6). Twenty-two tRNAs were located among the rRNAs and PCGs. The central conserved sequences of CSB-F, CSB-E and CSB-D were determined in the
Table 1. Characteristics of the mitochondrial genome of A. rivulatus. Location Locus Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu(UAA) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Start 1 70 1016 1088 2783 2857 3835 3904 3974 4043 5088
Codon Stop 69 1015 1087 2782 2856 3831 3904 3974 4042 5087 5159
Size of nucleotide (bp) 69 946 72 1695 74 975 70 71 69 1045 72
Amino acid
Start
Stop
324
ATG
TAA
348
ATG
T– –
Intergenic nucleotide* 0 0 0 0 0 3 1 1 0 0
Strand H H H H H H H L H H H (continued )
Correspondence: Zhijing Sun, Aquaculture Technology Research Laboratory, Tianjin Fisheries Research Institute, Tianjin 300221, People’s Republic of China. Tel: +86-22-88250594. Fax: +86-22-88252084. E-mail: [email protected]
2
C. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Location Locus
Downloaded by [Australian National University] at 07:23 06 November 2015
Ala
tRNA tRNAAsn tRNACys tRNATyr COI tRNASer(UGA) tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(GCU) tRNALeu(UAG) ND5 ND6 tRNAGlu Cytb tRNAThr tRNAPro D-loop
Codon
Start
Stop
Size of nucleotide (bp)
5161 5231 5340 5406 5477 7116 7189 7266 7957 8031 8189 8872 9656 9727 10,073 10,142 10,432 11,813 11,882 11,953 12,026 13,873 14,383 14,456 15,597 15,671 15,740
5229 5303 5405 5475 7039 7186 7261 7956 8029 8198 8871 9655 9726 10,072 10,141 10,438 11,812 11,881 11,948 12,025 13,864 14,382 14,451 15,592 15,668 15,739 16,585
69 73 66 70 1563 71 73 691 73 168 683 784 71 346 69 297 1381 69 67 73 1839 510 69 1137 72 69 846
Amino acid
Start
Stop
520
GTG
TAG
230
ATG
T– –
55 227 261
ATG ATG ATG
TAA TA– T– –
116
ATG
T– –
98 460
ATG ATG
TAA T– –
612 173
ATG ATG
TAG TAG
378
ATG
TAA
Intergenic nucleotide* 1 1 36 0 1 76 2 4 0 1 10 0 0 0 0 0 7 0 0 4 0 8 0 4 4 2 0
Strand 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 and L indicate heavy and light strands. *Numbers correspond to the nucleotides separating different genes, negative numbers represent the overlapping nucleotides.
positions 16,105–16,033, 16,065–16,091 and 16,106–16,128 bp. The conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were in the positions 16,377–16,398, 16,452–16,477 and 16,499– 16,524 bp, respectively.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. We acknowledge grant support from the Tianjin science and technology plan projects (12ZCZDNC01100, 14ZXNZNC00046) and Research Program of Application Foundation and Advanced Technology of Tianjin (11JCYBJC08800).
References Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Li CY, Li JT, Xiao GB, Hou GY, Sun XW. (2014). Complete mitochondrial genome of the kissing gourami, Helostoma temminkii. Mitochondrial DNA. [Epub ahead of print]. DOI: 10.3109/19401736. 2013.861451. Xue W, Hou GY, Li CY, Kong XF, Zheng XH, Li JT, Sun XW. (2013). Complete mitochondrial genome of Chinese sleeper, Perccottus glenii. Mitochondrial DNA 24:339–41.
