http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855907
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Thymallus grubii (Salmonidae: Thymallinae)
Mitochondrial DNA Downloaded from informahealthcare.com by Memorial University of Newfoundland on 05/25/14 For personal use only.
Bo Ma1, Haiying Jiang2, Peng Sun3, and Jinping Chen2 1
Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China, 2Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China, and 3College of Life Science and Technology, Harbin Normal University, Harbin, China
Abstract
Keywords
The complete mitochondrial DNA sequence of Thymallus grubii (Salmonidae: Thymallinae) was determined in this study. The complete mtDNA sequence of T. grubii was 16,657 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Intergenic spacer and overlapping sequences were found in mtDNA of T. grubii. The base composition of the whole mtDNA was 27.9% A, 27.2% T, 27.5% C and 17.4% G, with a slightly A þ T bias of 55.1%. Seven protein-coding genes had an incomplete stop codon in T. grubii.
Amur grayling, fish, mitochondrial genome, Thymallus grubii
The Amur grayling, Thymallus grubii, is an important commercial cold freshwater fish and mainly distributed in the Amur basin and limited to the upper levels of some rivers in China (Ma et al., 2012). Nowadays, mitochondrial DNA (mtDNA) has been widely used for molecular identification and phylogenetic analysis of closely related species. Up to date, only two Thymallus complete mtDNA had been sequenced: Thymallus thymallus (NC_012928.1) and Thymallus arcticus (NC_012929.1). However, there was no data of the complete mitochondrial genome of Thymallus grubii. In this study, the whole mitochondrial genome sequence of T. grubii was characterized using polymerase chain reaction (PCR)-based method (GenBank accession number: KF692113). The genes were annotated using MitoFish online version available at http://mitofish.aori.utokyo.ac.jp/annotation/input.html (Iwasaki et al., 2013). The sequence alignment was performed by Clustal Omega (Sievers et al., 2011). The complete mtDNA sequences of Thymallus grubii was a circular molecule of 16,657 bp in length, including
Correspondence: J. Chen, Guangdong Entomological Institute/ South China Institute of Endangered Animals, Guangzhou, 510260, China. Tel: 86-20-89100920. Fax: 86-20-84183704. E-mail: [email protected]
History Received 25 September 2013 Accepted 29 September 2013 Published online 10 January 2014
13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 1 control region (D-loop). Its organization and arrangement was presented in Table 1, which was identical to the other fish mitochondrial genomes (Hwang et al., 2013; Liang et al., 2012; Wang et al., 2013; Yasuike et al., 2010). The base composition of the whole mtDNA was 27.9% A, 27.2% T, 27.5% C and 17.4% G, with a slightly A þ T bias of 55.1%. All protein-coding genes used ATG as the start codon with exception of CO1 which used GTG. Five protein-coding genes terminated with the complete stop codon TAA (ND1, CO1, ATPase8, ND4L and ND5), ND6 regarded TAG as stop codon and the rest showed an incomplete stop codon (T or TA), which was quite common among other fishes (Hwang et al., 2013; Liang et al., 2012; Wang et al., 2013). Some overlapping sequences were found among the 13 protein-coding genes: ATPase8 gene overlapped with ATPase6 gene for 10 bp, ND4L gene overlapped with ND4 gene for 7 bp and ND6 gene overlapped with ND5 gene for 4 bp. On the other hand, some intergenic spacers were found in T. grubii mtDNA. The 22 tRNA genes ranged in length from 67 bp (tRNA-Cys) to 75 bp (tRNA-Leu), and were predicted to fold into expected cloverleaf secondary structures. The 12S and 16S rRNA genes were 947 and 1679 bp, respectively, located between the tRNA-Phe and tRNA-Leu (UUA) genes and separated by the tRNA-Val gene. The control region of T. grubii was 997 bp in length and lied between the tRNA-Pro and tRNA-Phe genes. The origin of light-strand replication was identified between tRNA-Asn and tRNA-Cys genes and was 34 bp in length. The sequence alignment showed that the mtDNA of T. grubii shared 94.71 and 94.47% sequence identity with that of T. arcticus (NC_012929.1) and T. thymallus (NC_012928.1), respectively.
2
B. Mo et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of Thymallus grubii.
Mitochondrial DNA Downloaded from informahealthcare.com by Memorial University of Newfoundland on 05/25/14 For personal use only.
Gene name
Coding strand
Start position
End position
Intergenic nucleotidesa (bp)
Size (bp)
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
1 69 1016 1088 2767 2842 3825 3894 3964 4033 5081 5154 5224 5331 5398 5470 7021 7096 7184 7875 7950 8108 8791 9576 9646 9995 10,065 10,355 11,736 11,805 11,876 11,949 13,784 14,306 14,379 15,520 15,591 15,661
68 1015 1087 2766 2841 3816 3896 3964 4032 5080 5152 5222 5296 5397 5468 7020 7091 7169 7874 7948 8117 8790 9575 9645 9994 10,064 10,361 11,735 11,804 11,874 11,948 13,787 14,305 14,374 15,519 15,591 15,660 16,657
0 0 0 0 0 8 3 1 0 0 1 1 34 0 1 0 4 14 0 1 10 0 0 0 0 0 7 0 0 1 0 4 0 4 0 1 0
68 947 72 1679 75 975 72 71 69 1048 72 69 73 67 71 1551 71 74 691 74 168 683 785 70 349 70 297 1381 69 70 73 1839 522 69 1141 72 70 997
tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr CO1 tRNA-Ser(UCA) tRNA-Asp CO2 tRNA-Lys ATPase8 ATPase6 CO3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGC) tRNA-Leu(CUA) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
No. of codons
Start codon
Stop codonb
324
ATG
TAA
349
ATG
T
516
GTG
TAA
230
ATG
T
55 227 261
ATG ATG ATG
TAA TA TA
116
ATG
T
98 460
ATG ATG
TAA T
612 173
ATG ATG
TAA TAG
380
ATG
T
a
Numbers corresponded to the nucleotides separating adjacent genes; Negative numbers indicated overlapping nucleotides. T and TA represented incomplete stop codons.
b
We believed that this study could provide a useful data for molecular identification and phylogenetic analysis of Thymallus fishes.
Acknowledgements We thank Li Linmiao and Wang Hui from Guangdong Entomological Institute for their lab assistant for this work.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article paper. This study was funded and supported by the Special Scientific Research Funds for Central Non-profit Institutes from Chinese Academy of Fishery Sciences, China (2013A01) and the Science and Technology Planning Project of Guangdong Province, China (2011B090300024).
References Hwang DS, Lee WO, Lee JS. (2013). Complete mitochondrial genome of the freshwater fish, Acanthorhodeus macropterus (Cypriniformes,
Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.775265. 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. Liang HW, Hu GF, Li Z, Zou GW, Liu XL. (2012). Mitochondrial DNA sequence of yellow catfish (Pelteobagrus fulvidraco). Mitochondrial DNA 23:170–2. Ma B, Lui T, Zhang Y, Chen J. (2012). Phylogeography and population genetic structure of Amur Grayling Thymallus grubii in the Amur Basin. Asian-Aust J Anim Sci 25:935–44. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. doi:10.1038/msb.2011.75. Wang H, Zhang B, Li L, Chen J. (2013). The complete mitochondrial genome of the Acipenser schrenckii (Acipenseridae: Acipenser). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2013.815174. Yasuike M, Jantzen S, Cooper G, Leder E, Davidson W, Koop B. (2010). Grayling (Thymallinae) phylogeny within salmonids: Complete mitochondrial DNA sequences of Thymallus arcticus and Thymallus thymallus. J Fish Biol 76:395–400.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Thymallus grubii (Salmonidae: Thymallinae)
Mitochondrial DNA Downloaded from informahealthcare.com by Memorial University of Newfoundland on 05/25/14 For personal use only.
Bo Ma1, Haiying Jiang2, Peng Sun3, and Jinping Chen2 1
Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China, 2Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China, and 3College of Life Science and Technology, Harbin Normal University, Harbin, China
Abstract
Keywords
The complete mitochondrial DNA sequence of Thymallus grubii (Salmonidae: Thymallinae) was determined in this study. The complete mtDNA sequence of T. grubii was 16,657 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Intergenic spacer and overlapping sequences were found in mtDNA of T. grubii. The base composition of the whole mtDNA was 27.9% A, 27.2% T, 27.5% C and 17.4% G, with a slightly A þ T bias of 55.1%. Seven protein-coding genes had an incomplete stop codon in T. grubii.
Amur grayling, fish, mitochondrial genome, Thymallus grubii
The Amur grayling, Thymallus grubii, is an important commercial cold freshwater fish and mainly distributed in the Amur basin and limited to the upper levels of some rivers in China (Ma et al., 2012). Nowadays, mitochondrial DNA (mtDNA) has been widely used for molecular identification and phylogenetic analysis of closely related species. Up to date, only two Thymallus complete mtDNA had been sequenced: Thymallus thymallus (NC_012928.1) and Thymallus arcticus (NC_012929.1). However, there was no data of the complete mitochondrial genome of Thymallus grubii. In this study, the whole mitochondrial genome sequence of T. grubii was characterized using polymerase chain reaction (PCR)-based method (GenBank accession number: KF692113). The genes were annotated using MitoFish online version available at http://mitofish.aori.utokyo.ac.jp/annotation/input.html (Iwasaki et al., 2013). The sequence alignment was performed by Clustal Omega (Sievers et al., 2011). The complete mtDNA sequences of Thymallus grubii was a circular molecule of 16,657 bp in length, including
Correspondence: J. Chen, Guangdong Entomological Institute/ South China Institute of Endangered Animals, Guangzhou, 510260, China. Tel: 86-20-89100920. Fax: 86-20-84183704. E-mail: [email protected]
History Received 25 September 2013 Accepted 29 September 2013 Published online 10 January 2014
13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA) and 1 control region (D-loop). Its organization and arrangement was presented in Table 1, which was identical to the other fish mitochondrial genomes (Hwang et al., 2013; Liang et al., 2012; Wang et al., 2013; Yasuike et al., 2010). The base composition of the whole mtDNA was 27.9% A, 27.2% T, 27.5% C and 17.4% G, with a slightly A þ T bias of 55.1%. All protein-coding genes used ATG as the start codon with exception of CO1 which used GTG. Five protein-coding genes terminated with the complete stop codon TAA (ND1, CO1, ATPase8, ND4L and ND5), ND6 regarded TAG as stop codon and the rest showed an incomplete stop codon (T or TA), which was quite common among other fishes (Hwang et al., 2013; Liang et al., 2012; Wang et al., 2013). Some overlapping sequences were found among the 13 protein-coding genes: ATPase8 gene overlapped with ATPase6 gene for 10 bp, ND4L gene overlapped with ND4 gene for 7 bp and ND6 gene overlapped with ND5 gene for 4 bp. On the other hand, some intergenic spacers were found in T. grubii mtDNA. The 22 tRNA genes ranged in length from 67 bp (tRNA-Cys) to 75 bp (tRNA-Leu), and were predicted to fold into expected cloverleaf secondary structures. The 12S and 16S rRNA genes were 947 and 1679 bp, respectively, located between the tRNA-Phe and tRNA-Leu (UUA) genes and separated by the tRNA-Val gene. The control region of T. grubii was 997 bp in length and lied between the tRNA-Pro and tRNA-Phe genes. The origin of light-strand replication was identified between tRNA-Asn and tRNA-Cys genes and was 34 bp in length. The sequence alignment showed that the mtDNA of T. grubii shared 94.71 and 94.47% sequence identity with that of T. arcticus (NC_012929.1) and T. thymallus (NC_012928.1), respectively.
2
B. Mo et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of Thymallus grubii.
Mitochondrial DNA Downloaded from informahealthcare.com by Memorial University of Newfoundland on 05/25/14 For personal use only.
Gene name
Coding strand
Start position
End position
Intergenic nucleotidesa (bp)
Size (bp)
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
1 69 1016 1088 2767 2842 3825 3894 3964 4033 5081 5154 5224 5331 5398 5470 7021 7096 7184 7875 7950 8108 8791 9576 9646 9995 10,065 10,355 11,736 11,805 11,876 11,949 13,784 14,306 14,379 15,520 15,591 15,661
68 1015 1087 2766 2841 3816 3896 3964 4032 5080 5152 5222 5296 5397 5468 7020 7091 7169 7874 7948 8117 8790 9575 9645 9994 10,064 10,361 11,735 11,804 11,874 11,948 13,787 14,305 14,374 15,519 15,591 15,660 16,657
0 0 0 0 0 8 3 1 0 0 1 1 34 0 1 0 4 14 0 1 10 0 0 0 0 0 7 0 0 1 0 4 0 4 0 1 0
68 947 72 1679 75 975 72 71 69 1048 72 69 73 67 71 1551 71 74 691 74 168 683 785 70 349 70 297 1381 69 70 73 1839 522 69 1141 72 70 997
tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu(UUA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr CO1 tRNA-Ser(UCA) tRNA-Asp CO2 tRNA-Lys ATPase8 ATPase6 CO3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser(AGC) tRNA-Leu(CUA) ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro D-loop
No. of codons
Start codon
Stop codonb
324
ATG
TAA
349
ATG
T
516
GTG
TAA
230
ATG
T
55 227 261
ATG ATG ATG
TAA TA TA
116
ATG
T
98 460
ATG ATG
TAA T
612 173
ATG ATG
TAA TAG
380
ATG
T
a
Numbers corresponded to the nucleotides separating adjacent genes; Negative numbers indicated overlapping nucleotides. T and TA represented incomplete stop codons.
b
We believed that this study could provide a useful data for molecular identification and phylogenetic analysis of Thymallus fishes.
Acknowledgements We thank Li Linmiao and Wang Hui from Guangdong Entomological Institute for their lab assistant for this work.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article paper. This study was funded and supported by the Special Scientific Research Funds for Central Non-profit Institutes from Chinese Academy of Fishery Sciences, China (2013A01) and the Science and Technology Planning Project of Guangdong Province, China (2011B090300024).
References Hwang DS, Lee WO, Lee JS. (2013). Complete mitochondrial genome of the freshwater fish, Acanthorhodeus macropterus (Cypriniformes,
Cyprinidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.775265. 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. Liang HW, Hu GF, Li Z, Zou GW, Liu XL. (2012). Mitochondrial DNA sequence of yellow catfish (Pelteobagrus fulvidraco). Mitochondrial DNA 23:170–2. Ma B, Lui T, Zhang Y, Chen J. (2012). Phylogeography and population genetic structure of Amur Grayling Thymallus grubii in the Amur Basin. Asian-Aust J Anim Sci 25:935–44. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. doi:10.1038/msb.2011.75. Wang H, Zhang B, Li L, Chen J. (2013). The complete mitochondrial genome of the Acipenser schrenckii (Acipenseridae: Acipenser). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/ 19401736.2013.815174. Yasuike M, Jantzen S, Cooper G, Leder E, Davidson W, Koop B. (2010). Grayling (Thymallinae) phylogeny within salmonids: Complete mitochondrial DNA sequences of Thymallus arcticus and Thymallus thymallus. J Fish Biol 76:395–400.
