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

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The complete mitochondrial genome sequence of Sinogastromyzon sichangensis (Cypriniformes, Balitoridae)

Dan Yu, Rong He & Qiongying Tang

To cite this article: Dan Yu, Rong He & Qiongying Tang (2015) The complete mitochondrial genome sequence of Sinogastromyzon sichangensis (Cypriniformes, Balitoridae), Mitochondrial DNA, 26:6, 859-860, DOI: 10.3109/19401736.2013.861430

To link to this article: http://dx.doi.org/10.3109/19401736.2013.861430

Published online: 10 Jan 2014.

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Download by: [Institute of Hydrobiology], [Dr Qiongying Tang] Date: 26 December 2015, At: 00:51 http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic)

Mitochondrial DNA, 2015; 26(6): 859–860 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.861430

MITOGENOME ANNOUNCEMENT The complete mitochondrial genome sequence of Sinogastromyzon sichangensis (Cypriniformes, Balitoridae)

Dan Yu1, Rong He2, and Qiongying Tang1

1The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China and 2Department of Fisheries, Southwest University, Rongchang, Chongqing, P.R. China

Abstract Keywords Sinogastromyzon sichangensis, belonging to the family Balitoridae in Cypriniformes, is endemic Balitoridae, mitogenome, phylogenetic to the Upper Yangtze River and the Qing River. In this study, the complete mitochondrial position, Sinogastromyzon sichangensis genome of S. sichangensis was sequenced with its structure analyzed. The mitochondrial genome of S. sichangensis is similar to those of the typical vertebrates, 16,567 bp in length, History including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one non-coding control region (D-loop). The D-loop of S. sichangensis was characterized by one Received 2 October 2013 termination-associated sequence and seven conserved sequence blocks (CSB-F, CSB-E, CSB-D, Revised 8 October 2013 CSB-B and CSB I-III). The mitogenome sequence of S. sichangensis could contribute to estimate Accepted 24 October 2013 the phylogenetic relationship of the Balitoridae. Further investigations with more Published online 10 January 2014 Sinogastromyzon species and other balitorid fishes included should be performed to better understand the evolutionary history of this unique group of fishes which can successfully adapt to mountain torrents.

The Balitoridae (referring to hillstream loaches) is a unique group Table 1. Organization of the mitochondrial genome of S. sichangensis. of Cypriniformes, their paired fins enlarged with adhesive pads on ventral surface, which make them be successfully adaptive to Position number Codon mountain torrents. Presently only five balitorid species mitogen- omes are sequenced, with one species Sinogastromyzon puliensis Size Intergenic Feature Start Stop (bp) Start Stop nucleotide* Strandy from Sinogastromyzon, the genus which has 21 valid species described so far (Froese & Pauly, 2013). The species tRNAPhe 16969 H 12S rRNA 70 1022 953 H Sinogastromyzon sichangensis (Cypriniformes, Balitoridae) is Val endemic to the Upper Yangtze River and the Qing River (Yue, tRNA 1023 1094 72 H 16S rRNA 1095 2775 1681 H 2000). In this study, we sequenced the complete mitochondrial tRNALeu(UUR) 2776 2850 75 H genome of S. sichangensis with the GenBank accession number ND1 2852 3826 975 ATG TAA –1 H KF711948. The live S. sichangensis individuals were collected tRNAIle 3830 3901 72 –3 H from Guizhou province of China. tRNAGln 3900 3970 71 þ2L Met The complete S. sichangensis mitogenome sequence was tRNA 3972 4040 69 –1 H 16,567 bp in length, and was composed of 13 protein-coding ND2 4041 5087 1047 ATG TAG H tRNATrp 5086 5155 70 þ2H genes (cyt b, ATP6, ATP8, COI-III, ND1-6 and ND4L), two rRNA Ala

Downloaded by [Institute of Hydrobiology], [Dr Qiongying Tang] at 00:51 26 December 2015 tRNA 5158 5226 69 –2 L genes (12S and 16S rRNA), 22 tRNA genes and one non-coding tRNAAsn 5228 5300 73 –1 L control region (CR), most of which were encoded on the H-strand, rep_origin 5301 5331 31 except for ND6 and eight tRNA genes (tRNAGln, tRNAAla, tRNACys 5332 5397 66 L tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro; tRNATyr 5399 5467 69 –1 L Table 1). These features were similar to mitogenome of COI 5469 7019 1551 GTG TAA –1 H tRNASer(UCN) 7021 7091 71 –1 L the typical vertebrates (He et al., 2011; Peng et al., 2006; tRNAAsp 7094 7166 73 –2 H Tang et al., 2013; Wang et al., 2012). The nucleotide composition COII 7181 7871 691 ATG T –14 H of S. sichangensis mitogenome was A – 30.3%, T – 25.2%, tRNALys 7872 7947 76 H C – 27.9% and G – 16.6%, with a slight A þT rich feature ATPase8 7949 8116 168 ATG TAA –1 H (55.5%). Almost all of the 13 protein-coding genes showed ATPase6 8107 8790 684 ATG TAA þ10 H COIII 8790 9575 786 ATG TAA þ1H tRNAGly 9575 9647 73 þ1H ND3 9648 9998 351 ATG TAG H Correspondence: Q. Tang, The Key Laboratory of Aquatic Biodiversity tRNAArg 9997 10,066 70 þ2H and Conservation of Chinese Academy of Sciences, Institute of ND4L 10,067 10,363 297 ATG TAA H Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China. Tel: +86-27-68780049. Fax: +86-27-68780065. E-mail: (continued ) [email protected] 860 D. Yu et al. Mitochondrial DNA, 2015; 26(6): 859–860

Table 1. Continued but many other aspects such as genetics and molecular phylogenetic relationship remains elusive. This work provides Position number Codon fundamental data for further phylogeography, population genetics, Size Intergenic and conversation genetics studies on this balitorid species. Feature Start Stop (bp) Start Stop nucleotide* Strandy Acknowledgements ND4 10,357 11,739 1383 ATG TAG þ7H tRNAHis 11739 11808 70 þ1HThe authors thank DeQing Tan and Yuyu Xiong for their help in tRNASer(AGN) 11,808 11,877 70 þ1Hcollecting samples. We also appreciate Sen He for his assistance with the tRNALeu(CUN) 11,878 11,950 73 H laboratory work. ND5 11,951 13,789 1839 ATG TAA H ND6 13,786 14,307 522 ATG TAA þ4LDeclaration of interest tRNAGlu 14,308 14,376 69 L Cytb 14,383 15,523 1141 ATG T –6 H The authors alone are responsible for the content and writing of the paper. tRNAThr 15,524 15,595 72 H This work was supported by the grants from the National Natural Science tRNAPro 15,597 15,666 70 –1 L Foundation of China (Grant No. 31272306 and 31061160185). D-Loop 15,667 16,567 901 H References * and þ represent the interval and overlap nucleotide between two adjacent genes, respectively. Clayton DA. (1991). Nuclear gadgets in mitochondrial DNA replication y L and H refer to light and heavy strands, respectively. and transcription. Trends Biochem Sci 16:107–11. Froese R, Pauly D. (2013). FishBase. Available at: www.fishbase.org, version (Accessed August 2013). the regular initiation codon ATG with the only exception of He AY, Luo YJ, Yang H, Liu LP, Li SF, Wang CH. (2011). Complete COI which started with GTG. Eleven protein-coding genes mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome character- shared the typical stop codons (TAA for eight genes and TAG ization and phylogeny applications. Mol Biol Rep 38:2015–21. for three genes), and the remaining two (COII and cyt b) Liu HZ. (2002). Structure and evolution of fish mitochondrial control possessed incomplete stop codons with a terminal T. The D-loop region, bitterlings as example. Prog Nat Sci 12:266–70. was 901 bp long, and its base composition was A – 34.2%, Peng ZG, Wang J, He SP. (2006). The complete mitochondrial genome of T – 32.5%, C – 18.9% and G – 14.4%, reflecting a strong rich the helmet catfish Cranoglanis bouderius (Siluriformes: feature in A and T (A þT ¼ 66.7%). The termination-associated Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376: 290–7. sequence was identified, and two motifs, ‘‘TACAT’’ and its Shadel GS, Clayton DA. (1997). Mitochondrial DNA maintenance in reverted and complemented sequence ‘‘ATGTA’’ could be vertebrates. Annu Rev Biochem 66:409–35. found; four central conserved sequences (CSB-F, CSB-E, CSB- Tang QY, Huang Y, Wang JJ, Huang J, Wang ZJ, Peng ZG. (2013). The B and CSB-D) were also identified by following Liu (2002); three complete mitochondrial genome sequence of Triplophysa bleekeri conserved sequence blocks (CSB I–III) could be easily identified, (Teleostei, Balitoridae, Nemacheilinae). Mitochondrial DNA 24:25–7. which were thought to be involved in positioning RNA Wang JJ, Tang QY, Wang ZJ, Zhang YG, Wu Q, Peng ZG. (2012). The Triplophysa rosa polymerase both for transcription and for priming replication complete mitogenome sequence of a cave loach (Teleostei, Balitoridae, Nemacheilinae). Mitochondrial DNA 23: (Clayton, 1991; Shadel & Clayton, 1997). 366–8. Currently some detailed studies on the genus Yue PQ. (2000). Fauna sinica. Osteichthyes. Cypriniformes III. Beijing: Sinogastromyzon’s taxonomy and biology have been carried out, Sciences Press. Downloaded by [Institute of Hydrobiology], [Dr Qiongying Tang] at 00:51 26 December 2015