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

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The complete mitochondrial genome sequence of Tor sinensis (Cypriniformes, Cyprinidae) Fujiang Huang, Mingdian Liu, Chao Ye & Shaoping Liu To cite this article: Fujiang Huang, Mingdian Liu, Chao Ye & Shaoping Liu (2015) The complete mitochondrial genome sequence of Tor sinensis (Cypriniformes, Cyprinidae), Mitochondrial DNA, 26:5, 712-713, DOI: 10.3109/19401736.2013.843087 To link to this article: http://dx.doi.org/10.3109/19401736.2013.843087

Published online: 11 Dec 2013.

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Date: 06 November 2015, At: 09:15

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(5): 712–713 ! 2013 Informa UK Ltd. DOI: 10.3109/19401736.2013.843087

MITOGENOME ANNOUNCEMENT

The complete mitochondrial genome sequence of Tor sinensis (Cypriniformes, Cyprinidae) Fujiang Huang1, Mingdian Liu1, Chao Ye1,2, and Shaoping Liu1

Downloaded by [University of California, San Diego] at 09:15 06 November 2015

1

Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture, Wuhan, China and 2Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, School of Life Science, Southwest University, Chongqing, China Abstract

Keywords

The complete mitogenome sequence of Tor sinensis was determined using long PCR reactions. The genome is 16,579 bp in length, including 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The gene order and composition of T. sinensis was similar to that of most other vertebrates. The descending order of the base composition on heavy strand was 31.9% A, 27.4% C, 24.9% T, 15.7% G, with a relatively lower level of G and a slight AT bias of 56.8%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). There are 9 regions of gene overlap totaling 29 bp and 14 inter-genic spacer regions totaling 71 bp.

Cypriniformes, mitogenome, Tor sinensis

Here, we presented the complete mitochondrial genome of Tor sinensis that was deposited in GenBank with the accession number KF305826. We annotated the DNA sequence with a Web-based tool DOGMA (Wyman et al., 2004), which has ever been used in many previous studies. Initially, we amplified and sequenced the whole mitochondrial genome sequence of T. sinensis 10 pairs of primers designed in accordance with equivalent mitochondrial genome sequences of 30 species from Cypriniformes (Wang et al., 2011). Subsequently, we designed two additional pairs of the species-specific primers for the two gaps based on the previously sequenced data so as to

History Received 6 September 2013 Accepted 7 September 2013 Published online 11 December 2013

gain the whole mitogenome sequence. All the primers were available upon request. The complete mitochondrial genome of T. sinensis was found to be similar to that of most other vertebrates (e.g. Huang et al., 2012; Wang et al., 2008). It was sequenced and determined to be 16,579 bp in length, including 13 typical vertebrate proteincoding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region (Table 1). Except for ND6 gene and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro), all other genes were encoded on the H-strand. The base composition was analyzed by using MEGA5

Table 1. Characteristics of the mitochondrial genome of T. sinensis. Codon Gene/element

From

tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn

1 70 1026 1098 2777 2854 3833 3903 3975 4044 5089 5163 5234

To 69 1025 1097 2776 2852 3828 3904 3973 4043 5090 5160 5232 5306

Length (bp) 69 956 72 1679 76 975 72 71 69 1047 72 70 73

Start

Stop

ATG

TAA

ATG

TAG

Inter-genic nucleotidesa 0 0 0 0 1 4 2 1 0 2 2 1

Strandb H H H H H H H L H H H L L (continued )

Correspondence: Shaoping Liu, Yangtze River Fisheries Research Institute of Chinese Academy of Fishery Science, Scientific Observing and Experimental Station of Fishery and Environment in the Upper and Middle Reaches of the Yangtze River, Ministry of Agriculture, No. 8, 1st Wudayuan Road, East Lake Hi-Tech Development Zone, Wuhan, Hubei 430223, P.R. China. Tel: +86 027 81780238. Fax: +86 027 81780238. E-mail: [email protected]

Complete mitochondrial genome sequence of Tor sinensis

DOI: 10.3109/19401736.2013.843087

713

Table 1. Continued.

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Codon Gene/element

From

To

Length (bp)

tRNACys tRNATyr COI tRNASer(UCN) tRNAAsp COII tRNALys ATPase 8 ATPase 6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro D-loop

5342 5410 5482 7033 7106 7190 7877 7958 8116 8799 9584 9656 10,005 10,075 10,365 11,746 11,815 11,885 11,961 13,781 14,303 14,376 15,517 15,588 15,658

5407 5480 7032 7103 7176 7880 7956 8122 8799 9584 9655 10,004 10,074 10,371 11,745 11,814 11,883 11,957 13,784 14,302 14,371 15,516 15,588 15,657 16,579

66 71 1551 71 71 691 80 165 684 786 72 349 70 297 1381 69 69 73 1824 522 69 1141 72 70 922

Start

Stop

GTG

TAA

ATG

T

ATG ATG ATG

TAG TAA TAA

ATG

T

ATG ATG

TAA T

ATG ATG

TAA TAA

ATG

T

Inter-genic nucleotidesa

Strandb

35 2 1 0 2 13 4 1 7 1 1 0 0 0 7 0 0 1 3 4 0 4 0 1 0

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

Negative numbers indicate overlapping nucleotides between adjacent genes. Numbers correspond to the nucleotides separating different genes. b H and L denote heavy and light strands. a

(Tamura et al., 2011). The base composition of H-strand was as follows 31.9% A, 27.4% C, 24.9% T and 15.7% G and AT content was 56.8%. The relative order of nucleotide composition matches with the nucleotide pattern of other cyprinids in the order: A4C4T4G (Wang, 2008). The GC content of cyprinid mitochondrial genomes is always lower than AT content and this is also evident in other teleost species (Cui, 2009; Yue, 2006). Of the 13 protein-coding genes, gene overlaps can be observed between four pairs of the contiguous genes, ATP8–ATP6, ATP6– COIII, ND4L–ND4 and ND5–ND6, and they overlap by seven, one, seven and four nucleotides, respectively, and 71 bp intergenic nucleotides in the whole genome, ranging from 1 to 35 bp (Table 1). The common start codon ATG was observed in all mitochondrial protein-coding genes except in the COI gene starting from GTG. Although three types of stop codons were used in the protein-coding genes, including two complete codons, TAA for ND1, COI, ATP6, COIII, ND4L, ND5 and ND6 genes; TAG for ND2 and ATP8 genes; and an incomplete one, T- for COII, ND3, ND4 and cytb genes, an incomplete stop codon as a common mark for stopping protein translations was also observed in many other fish species (e.g. Kartavtsev et al., 2007; Peng et al., 2006). The species T. Sinensis distributed in the lower reach of Lancang River (upper of Mekong River basin). Tor sinensis is also one of the most famous economic fishes of Yunnan province in southwest China. However, the genetic resources for this species are limited and the molecular systematics for this group of fishes remains elusive. We expect that this study could contribute to the accumulation of genetic resources for the species, so as to explore the evolutionary relationship between Cyprinidae and cypriniformes species in general.

Acknowledgements The authors thank Xiuhui Ma for the assistance with the laboratory work.

Declaration of interest This work was supported by the National Natural Science Foundation of China (31201997). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article.

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