Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis

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The complete mitochondrial genome of the Thymallus grubii (Amur grayling) Ji-Wei Zhao To cite this article: Ji-Wei Zhao (2015) The complete mitochondrial genome of the Thymallus grubii (Amur grayling), Mitochondrial DNA, 26:5, 799-800, DOI: 10.3109/19401736.2013.855899 To link to this article: http://dx.doi.org/10.3109/19401736.2013.855899

Published online: 10 Jan 2014.

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Date: 06 November 2015, At: 06:03

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 799–800 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.855899

MITOGENOME ANNOUNCEMENT

The complete mitochondrial genome of the Thymallus grubii (Amur grayling) Ji-Wei Zhao

Downloaded by [Chinese University of Hong Kong] at 06:03 06 November 2015

Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, People’s Republic of China

Abstract

Keywords

In this study, we reported the complete sequence of mitochondrial genome of Thymallus grubii. The complete mitochondrial genome sequence was determined to be 16,662 bp in length and contain 13 protein-coding genes, 22 tRNA genes, 2 ribosomal genes, the control region and the origin of light-strand replication. In control region, only four CSBs (CSB-1, CSB-2, CSB-3 and CSB-F) were identified.

Mitochondrial genome sequence, protein-coding genes, Thymallus grubii

As a kind of small economic fish and belongs to the Thymallidae family within the Salmoniformes, commonly known as speckled trout, Amur grayling is a freshwater resident salmonid throughout Europe, Asia and North America. And it is widely distributed in the Amur River, Mutankiang, Ussuri River, Songhua River and Razdolnaya River in China. The complete mitochondrial genomes of many species and subspecies from Salmoniformes have been reported. However, no mitogenome of Thymallus grubii is available until now. In this study, we reported the complete sequence of the mitochondrial genome of T. grubii. The samples of T. grubii were collected from Amur River (Heilongjiang Province, China). Genomic DNA was extracted using a DNeasy Tissue Kit (Qiagen, Valencia, CA). The complete mitochondrial genome were amplified and sequenced with Shin et al. (2012) method. The whole mitochondrial genome of T. grubii (GenBank accession number: KF649073) was 16,662 bp in length, including the control region (CR), the origin of light-strand replication (OL), 22 tRNA, 2 rRNA and 13 protein-coding genes (PCGs) (Table 1). There were 10 overlapping regions and 9 intergenic spacers among the genes. The overall base composition was 27.96% A, 27.09% T, 27.57% C, 17.39% G, with an AT content of 55.05%, which was similar with T. arcticus (AT 55.64%) and T. thymallus (AT 55.15%). The CR contained the conserved sequence blocks CSB1 (640–658), CSB2 (742–758) and CSB3

History Received 15 September 2013 Accepted 21 September 2013 Published online 10 January 2014

(783–797) and the critical central conserved sequences of CSB-F (306–323). CSB-D and CSB-E were not found. The OL sequence was similar to the OL sequences in the mitochondrial genomes of most vertebrates, and particularly in some fishes (Kartavtsev et al., 2007; Kim et al., 2004). It had the potential to fold in a stem-loop secondary structure with a stem formed by 12 paired nucleotides and a loop of 12 nucleotides. The sequence is 50 -CCGGGGCTTTCCCCCGCCTCG CCACCCTGTGGCGGGGGAAAGTAGA-30 . About 22 transfer RNA genes were interspersed between the rRNA and proteincoding genes, ranging in size from 68 bp (tRNA-Phe) to 75 bp (tRNA-Leu). The length of 12S rRNA and 16S rRNA was 947 bp and 1679 bp, respectively. All PCGs started with the orthodox initiation codon ATG, except for COX1, which began with GTG. The 4 PCGs (COX2, ND3, ND4 and Cytb) ended with a partial stop codon T. One gene (ND6) ended with TAG, and the remaining genes ended with TAA. The whole genome sequence similarity between T. grubii and T. arcticus (GenBank accession number: FJ872559), T. thymallus (GenBank accession number: FJ853655), B. lenok (GenBank accession number: JQ686731) and P. perryi (GenBank accession number: KC897653) was 94.6%, 94.5%, 86.5% and 86.0%, respectively. The gene arrangement among the five species was identical. The data would facilitate further investigations of phylogenetic relationships within Thymallus.

Correspondence: Ji-Wei Zhao, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, People’s Republic of China. Tel: +86 451 84869341. Fax: +86 451 84604803. E-mail: [email protected]

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J.-W. Zhao

Mitochondrial DNA, 2015; 26(5): 799–800

Table 1. Mitogenome organization of T. grubii. Location

Downloaded by [Chinese University of Hong Kong] at 06:03 06 November 2015

Gene Control region tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL tRNA-Cys tRNA-Tyr COX1 tRNA-Ser tRNA-Asp COX2 tRNA-Lys ATP8 ATP6 COX3 tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu Cytb tRNA-Thr tRNA-Pro

Size

Start

End

Nucleotide (bp)

1 1004 1072 2019 2091 3770 3845 4828 4897 4967 5036 6084 6157 6227 6296 6333 6400 6472 8023 8098 8186 8877 8952 9110 9793 10,578 10,648 10,997 11,067 11,357 12,738 12,807 12,878 12,951 14,786 15,308 15,381 16,522 16,593

1003 1071 2018 2090 3769 3844 4819 4899 4967 5035 6085 6155 6225 6299 6341 6399 6470 8022 8093 8171 8876 8950 9119 9793 10,578 10,647 10,996 11,066 11,363 12,737 12,806 12,876 12,950 14,789 15,307 15,376 16,521 16,593 16,662

1003 68 947 72 1679 75 975 72 71 69 1050 72 69 73 46 67 71 1551 71 74 691 74 168 684 786 70 349 70 297 1381 69 70 73 1839 522 69 1141 72 70

Codon Amino acid

Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article. This work was supported by the non-profit Scientific Research Institutes Special Funds (2007HSYZX-YZ-01).

References Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. (2007). Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and

325

350

517 231 56 228 262 117 99 461

613 174 381

Strand H 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

Start

End

ATG

TAA

ATG

TAA

GTG

TAA

ATG

T

ATG ATG ATG

TAA TAA TAA

ATG

T

ATG ATG

TAA T

ATG ATG

TAA TAG

ATG

T

Intergenic nucleotide (bp) 0 0 0 0 0 0 8 3 1 0 2 1 1 4 7 0 1 0 4 14 0 1 10 1 1 0 0 0 7 0 0 1 0 4 0 4 0 0

phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene 396:13–27. Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. (2004). The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobiidae) and phylogenetic considerations. Gene 336:147–53. Shin SC, Cho J, Lee JK, Ahn DH, Lee H, Park H. (2012). Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, amphipod). Mitochondrial DNA 23:25–7.

The complete mitochondrial genome of the Thymallus grubii (Amur grayling).

In this study, we reported the complete sequence of mitochondrial genome of Thymallus grubii. The complete mitochondrial genome sequence was determine...
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