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

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Sequencing, description and phylogenetic analysis of the mitochondrial genome of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae) Chen Li, Liping He, Chong Chen, Lingchao Cai, Pingping Chen & Shoubao Yang To cite this article: Chen Li, Liping He, Chong Chen, Lingchao Cai, Pingping Chen & Shoubao Yang (2014): Sequencing, description and phylogenetic analysis of the mitochondrial genome of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.928865

Published online: 24 Jun 2014.

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Date: 06 November 2015, At: 21:04

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.928865

MITOGENOME ANNOUNCEMENT

Sequencing, description and phylogenetic analysis of the mitochondrial genome of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae) Chen Li*, Liping He*, Chong Chen, Lingchao Cai, Pingping Chen, and Shoubao Yang

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College of life Sciences, Shaoxing University, Shaoxing, P.R. China

Abstract

Keywords

Sarcocheilichthys sinensis sinensis (Bleeker, 1871), is a small benthopelagic freshwater species with high nutritional and ornamental value. In this study, the complete mitochondrial genome of S. sinensis sinensis was determined; the phylogenetic analysis with another individual and closely related species of Sarcocheilichthys fishes was carried out. The complete mitogenome of S. sinensis sinensis was 16683 bp in length, consist of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: (D-loop and OL). It indicated that D-loop, ND2, and CytB may be appropriate molecular markers for studying population genetics and conservation biology of Sarcocheilichthys fishes.

Genetics, mitogenome, Sarcocheilichthys sinensis sinensis, sequencing

Sarcocheilichthys sinensis sinensis (Bleeker, 1871), also named Chinese lake gudgeon, is a benthopelagic freshwater species distributed widely in China (Song & Ma, 1994; Yuan et al., 2010), and is also a species with high nutritional as well as ornamental value (Li et al., 2011). The mitochondrial genome sequence can be useful data in genetics, evolution study as well as the sustainable utilization of many kinds of aquatic species (Liu & Cui, 2009; Wang et al., 2013; Yang et al., 2013). The primers used in this study to clone the complete mitochondrial genome sequence from Sarcocheilichthys sinensis sinensis (designated SS-1) were designed based on comparison of the complete mitochondrial genome of Sarcocheilichthys sinensis sinensis (GenBank accession no: KC847084, designated SS-2; Yang et al., 2013) and Sarcocheilichthys sinensis (GenBank accession no: NC_022475, designated SS-3), which were different individuals of the same species that distributed at different places. The complete mitochondrial genome of Sarcocheilichthys sinensis sinensis (designated SS-3) was sequenced and determined (16,683 bp in length, GenBank accession no. KJ850307), which consists of 13 protein-coding genes (PCDs), 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions (Table 1). Among these genes, 12 PCDs genes (ND1, ND2, COXI, COXII, ATP8, ATP6, COXIII, ND3, ND4L, ND4, ND5, and CytB), 2 rRNA genes (16S rRNA, and 12S rRNA), 14 tRNA genes (tRNAPhe, tRNAVal, tRNALeu(UUR), tRNAIle, tRNAMet, tRNATrp, tRNAAsp, tRNALys, tRNAGly, tRNAArg, tRNAHis, tRNASer(AGY), tRNALeu(CUN), and

*Both the authors have contributed equally to this work. Correspondence: Shoubao Yang, College of life Sciences, Shaoxing University, Shaoxing 312000, P.R. China. Tel/Fax: +86 57588342955. E-mail: [email protected]

History Received 20 May 2014 Accepted 25 May 2014 Published online 24 June 2014

tRNAThr) were encoded on the H-strand, while other genes were encoded on the L-strand. The arrangement of all of these genes was similar to other vertebrate species (Jondeung & Karinthanyakit, 2010). Totally, 21 variable sites (21 base substitutions) were detected between S. sinensis sinensis (SS-1) and S. sinensis (SS-2) through sequence comparison analysis, accounted for about 0.13% sites of the complete mitogenome sequence. These substitutions were distributed in most of PCDs (except for ATP8 and ND3), three tRNA genes (tRNAGln, tRNATrp, and tRNAThr) and a non-coding region (D-loop). Among them, two PCDs (ND2, and CytB) had relatively higher variable sites with two and four variable sites, respectively. Furthermore, two indels were only detected in D-loop which had three variable sites, indicating that D-Loop region evolves much faster than other regions of the mitochondrial genome. The result reveals that two PCDs (ND2, and CytB) and control region (D-Loop) might be useful molecular markers in studying population genetics and conservation biology of S. sinensis sinensis. Phylogenetic tree of Sarcocheilichthys fishes was constructed based on the complete mitochondrial genome sequences of S. sinensis sinensis (GenBank accession no: KJ850307, designated, SS-1), S. sinensis sinensis (GenBank accession no: KC847084, designated SS-2), Sarcocheilichthys sinensis (GenBank accession no: NC_022475, designated SS-3), Sarcocheilichthys lacustris (GenBank accession no: KF587906), Sarcocheilichthys nigripinnis (NC_020608), Sarcocheilichthys variegatus (GenBank accession no: AB569182), and Sarcocheilichthys parvus (GenBank accession no: NC_018786) using the neighbor-joining method (figure not shown). It shows that S. sinensis sinensis (SS-1) is clustered with SS-2 and SS-3, while S. nigripinnis, S. variegatus, S. parvus, and S. lacustris formed another monophyletic group. Present study provides useful data to population genetics and conservation biology of Sarcocheilichthys fishes.

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Table 1. Organization of the mitochondrial genome of S. sinensis sinensis.

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Locus tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet 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

Position

Size Nucleotide (bp)

From

To

1 70 1030 1102 2787 2864 3843 3913 3985 4054 5100 5173 5243 5316 5346 5416 5488 7039 7113 7196 7887 7964 8122 8805 9589 9661 10,011 10,081 10,371 11,753 11,822 11,892 11,965 13,797 14,319 14,389 15,533 15,604 15,674

69 1029 1101 2786 2862 3838 3914 3983 4053 5099 5170 5241 5315 5345 5413 5486 7038 7109 7184 7886 7962 8128 8805 9588 9660 10,010 10,080 10,377 11,752 11,821 11,890 11,964 13,800 14,318 14,387 15,532 15,604 15,673 16,683

Codon Start

69 960 72 1685 76 975 72 71 69 1046 71 69 73 30 68 71 1551 71 72 691 76 165 684 784 72 350 70 297 1382 69 69 73 1836 522 69 1144 72 70 1010

Amino acid

Anti-codon

Intergenic nucleotide

Strand

GAA

0 0 0 0 1 4 2 1 0 0 2 1 0 0 2 1 0 3 11 0 1 7 1 0 0 0 0 7 0 0 1 0 4 0 1 0 1 0

H H H H H H H L H H H L L

Stop

TAC TAA ATG

TAA

324 GAT TTG CAT

ATG

TA–

348 TCA TGC GTT GCA GTA

GTG

TAA

516 TGA GTC

ATG

T– –

230

ATG ATG ATG

TAA TAA T– –

54 227 261

ATG

TA–

116

ATG ATG

TAA TA–

98 460

TTT

TCC TCG GTG TAG ATG ATG

TAA TAA

611 173

ATG

T– –

380

TTC

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 Public Welfare Project of Science Technology Department of Zhejiang province (2011C22084); Student Innovation Training Program of Shaoxing University (2013).

References Jondeung A, Karinthanyakit W. (2010). The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes. Mitochondrial DNA 21:36–47. Li SM, Liang ZQ, Wu YA, Zeng CF, Li H, Ding DM, Liu MQ, Li CW. (2011). Analysis and Evaluation of Nutritional Components in the Muscle of Sarcocheilichthys sinensis sinensis Bleeker. J Anhui Agri Sci 39:19233–5.

TGT TGG

L L H L H H H H H H H H H H H H H H H L L H H L –

Liu Y, Cui Z. (2009).The complete mitochondrial genome sequence of the cutlassfish Trichiurus japonicus (Perciformes: Trichiuridae): Genome characterization and phylogenetic considerations.Mar Genomics 2: 133–42. Song TX, Ma J. (1994). Reproductive biology of Sarcocheilichthys sinensis. Zoological Reserch 15:96–102. Wang H, Li C, Yang XX, Yang SB, Han JW, He LP, Wei M, et al. (2013). Complete mitochondrial genome of Pseudobagrus ondon Shaw. Mitochondrial DNA [Epub ahead of print]. DOI: 10.3109/ 19401736.2013.834437. 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 [Epub ahead of print]. DOI: 10.3109/19401736.2013.796461. Yuan JL, Lian QP, Wang KW, Yao ZL, Lu YJ, Zhang AJ, Bi GQ. (2010). Seasonal variations of fish community structure in Lishui section of Oujiang River main stream. Chinese Journal of Ecology 29:1585–90.

Sequencing, description and phylogenetic analysis of the mitochondrial genome of Sarcocheilichthys sinensis sinensis (Cypriniformes: Cyprinidae).

Sarcocheilichthys sinensis sinensis (Bleeker, 1871), is a small benthopelagic freshwater species with high nutritional and ornamental value. In this s...
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