Skip to main content
SpringerLink
Log in

The complete mitochondrial genome of a threatened loach (Sinibotia reevesae) and its phylogeny

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

In present study, the complete mitochondrial genome of Sinibotia reevesae was first sequenced using the next-generation sequencing technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,572 bp in length, and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 displacement loop locus. It presents a typical gene organization and order for completely sequenced cypriniformes mitogenomes. The control region could be divided into three parts included the extended termination associated sequence domain, the central conserved domain and the conserved sequence block. Interestingly, two stem-loop domains were found in control region and OL region, respectively. Furthermore, phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Maximum likelihood and Bayesian analysis) both highly supported the close relationship of S. reevesae and Sinibotia superciliaris, which was in line with the previous classifications based on morphological and molecular studies. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105

    Article  CAS  PubMed  Google Scholar 

  • Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang HW (1944) Notes on the fishes of Western Szechwan and Eastern Sikang. Sincnsia 15:48–50

    Google Scholar 

  • Clayton DA (1992) Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol 141:217–232

    Article  CAS  PubMed  Google Scholar 

  • Ding RH (1994) The fishes of Sichuan. Sichuan Publishing House of Science and Technology, Chengdu (in Chinese)

    Google Scholar 

  • Jiang ZG, Jiang JP, Wang YZ, Zhang E, Zhang YY, Li LL, Xie F, Cai B, Cao L, Zheng GM et al (2016) Red list of China’s vertebrates. Biodivers Sci 24:500–551 (Chinese)

    Article  Google Scholar 

  • Laslett D, Canback B (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24:172–175

    Article  CAS  PubMed  Google Scholar 

  • Lavrov DV, Brown WM, Boore JL (2000) A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc Natl Acad Sci USA 97:13738–13742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li P, Yang C, Tu F, Liu G (2012) The complete mitochondrial genome of the Elongate loach Leptobotia elongata (Cypriniformes: Cobitidae). Mitochondrial DNA 23:352–354

    Article  CAS  PubMed  Google Scholar 

  • Liao F, Wang L, Wu S, Li YP, Zhao L, Huang GM, Niu CJ, Liu YQ, Li MG (2010) The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). Int J Biol Sci 6:172–186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274

    Article  CAS  PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manchado M, Catanese G, Ponce M, Funes V, Infante C (2007) The complete mitochondrial genome of the Senegal sole, Solea senegalensis Kaup. Comparative analysis of tandem repeats in the control region among soles. DNA Seq 18:169–175

    Article  CAS  PubMed  Google Scholar 

  • Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  CAS  PubMed  Google Scholar 

  • Meng XF, Shi M, Chen XX (2008) Population genetic structure of Chilo suppressalis (Walker) (Lepidoptera: Crambidae): strong subdivision in China inferred from microsatellite markers and mtDNA gene sequences. Mol Ecol 17:2880–2897

    Article  CAS  PubMed  Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  • Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, Packard M, Zhang Y, McClellan LR, Qi J et al (2009) The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res 19:213–220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mu X, Liu Y, Lai M, Song H, Wang X, Hu Y, Luo J (2015) Characterization of the Macropodus opercularis complete mitochondrial genome and family Channidae taxonomy using Illumina-based de novo transcriptome sequencing. Gene 559:189–195

    Article  CAS  PubMed  Google Scholar 

  • Nylander JAA (2004) MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre Uppsala University, Uppsala

    Google Scholar 

  • Ojala D, Merkel C, Gelfand R, Attardi G (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22:393–403

    Article  CAS  PubMed  Google Scholar 

  • Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358

    Article  CAS  PubMed  Google Scholar 

  • Powell AF, Barker FK, Lanyon SM (2013) Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study. Mol Phylogenet Evol 66:69–79

    Article  PubMed  Google Scholar 

  • Rambaut A (2009) FigTree, version 1.3. 1. Institute of Evolutionary Biology, University of Edinburgh. http://www.treebioedacuk/software/figtree/

  • Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinform 11:129

    Article  Google Scholar 

  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    Article  PubMed  PubMed Central  Google Scholar 

  • Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M (2006) Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826–841

  • Sbisa E, Tanzariello F, Reyes A, Pesole G, Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205:125–140

    Article  CAS  PubMed  Google Scholar 

  • Shen KN, Chen CH, Hsiao CD, Durand JD (2016a) Next-generation sequencing yields the complete mitochondrial genome of the flathead mullet, Mugil cephalus cryptic species in East Australia (Teleostei: Mugilidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:3218–3219

    CAS  PubMed  Google Scholar 

  • Shen KN, Yen TC, Chen CH, Li HY, Chen PL, Hsiao CD (2016b) Next generation sequencing yields the complete mitochondrial genome of the flathead mullet, Mugil cephalus cryptic species NWP2 (Teleostei: Mugilidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:1758–1759

    CAS  PubMed  Google Scholar 

  • Taanman JW (1999) The mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta 1410:103–123

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang QY, Liu HZ, Yang XP, Xiong BX (2005) Studies on the structure of the mitochondrial DNA control region and phylo genetic relationships of the subfamily Botiinae. Acta Hydrobiol Sin 29:645–653 (Chinese)

    CAS  Google Scholar 

  • Tang Q, Liu H, Mayden R, Xiong B (2006) Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol 39:347–357

    Article  CAS  PubMed  Google Scholar 

  • Tatarenkov A, Mesak F, Avise JC (2017) Complete mitochondrial genome of a self-fertilizing fish Kryptolebias marmoratus (Cyprinodontiformes, Rivulidae) from Florida. Mitochondrial DNA A DNA Mapp Seq Anal 28:244–245

    CAS  PubMed  Google Scholar 

  • Tian HW, Wang DQ, Jia XY, Duan XB, Chen DQ (2015) Complete mitochodrial genome of the redlip loach Leptobotia rubrilaris (Teleostei, Cypriniformes: Cobitidae). Mitochondrial DNA 26:668–669

  • Wan Q, Wei M, Yu P, Yang Y (2016) The complete mitochondrial genome of Parabotia banarescui (Cypriniformes: Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:1930–1931

  • Wang J, Yang G (2011) The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications. Mitochondrial DNA 22:120–129

    Article  PubMed  Google Scholar 

  • Wang YM, Xie BW, Wang F, Yue XJ, Wang Y, Qi ZM, Wu Y, Shen SY (2014) Reproductive characteristics of Sinibotia reevesae in the Tuojiang River. Chin J Zool 49:699–706 (Chinese)

    CAS  Google Scholar 

  • Wei M, Yu P, Yang Y, Wan Q (2016a) The complete mitochondrial genome of Leptobotia taeniaps (Cypriniformes: Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:1707–1708

    CAS  PubMed  Google Scholar 

  • Wei M, Yu P, Yang Y, Wan Q (2016b) The complete mitochondrial genome of Parabotia fasciata (Cypriniformes: Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:1831–1832

    CAS  PubMed  Google Scholar 

  • Wen ZY, Liang XF, He S, Li L, Shen D, Tao YX (2015) Molecular cloning and tissue expression of uncoupling protein 1, 2 and 3 genes in Chinese perch (Siniperca chuatsi). Comp Biochem Physiol B Biochem Mol Biol 185:24–33

    Article  CAS  PubMed  Google Scholar 

  • Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cytol 141:173–216

    Article  CAS  PubMed  Google Scholar 

  • Xie Z, Yu C, Guo L, Li M, Yong Z, Liu X, Meng Z, Lin H (2016) Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of black and reddish morphs of the Coral Trout Plectropomus leopardus. Mitochondrial DNA A DNA Mapp Seq Anal 27:609–612

    Article  CAS  PubMed  Google Scholar 

  • Yang B, Li C (2016) Characterization of the complete mitochondrial genome of the storage mite pest Tyrophagus longior (Gervais) (Acari: Acaridae) and comparative mitogenomic analysis of four acarid mites. Gene 576:807–819

    Article  CAS  PubMed  Google Scholar 

  • Yang ZY, Liang HW, Li Z, Wang XY, Zou GW (2013) Mitochondrial genome sequence of the Botia superciliaris (Teleostei, Cypriniformes). Mitochondrial DNA 24:347–349

    Article  CAS  PubMed  Google Scholar 

  • Yang ZT, Xiao SB, Liu M, Liao YS, Lu BQ, Sun JJ, Liu L (2016) The mitochondrial genome of Sinibotia robusta of pearl river (Cypriniformes: Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 27:4403–4404

    CAS  PubMed  Google Scholar 

  • Yu JN, Kwak M (2015) The complete mitochondrial genome of Brachymystax lenok tsinlingensis (Salmoninae, Salmonidae) and its intraspecific variation. Gene 573:246–253

    Article  CAS  PubMed  Google Scholar 

  • Yu P, Yang QC, Ding SQ, Zhang J, Li XL, Bi ZH, Wan Q (2016) The complete sequence of mitochondrial genome of Sinibotia pulchra (Cypriniformes: Cobitidae). Mitochondrial DNA A DNA Mapp Seq Anal 27(6):4318–4319

    CAS  PubMed  Google Scholar 

  • Zardoya R, Garrido-Pertierra A, Bautista JM (1995) The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J Mol Evol 41:942–951

    CAS  PubMed  Google Scholar 

  • Zhan W, Chen RY, Shen KN, Xu DD, Hsiao CD, Lou B (2017) Next-generation sequencing yields the complete mitochondrial genome of the Redbelly yellowtail fusilier, Caesio cuning (Teleostei: Caesionidae). Mitochondrial DNA A DNA Mapp Seq Anal 28:125–126

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Funds (No. 31402305), the Educational Commission of Sichuan Province of China (No. KYTD201009; No. 15ZA0285), the department of science and technology of Sichuan Province of China (No. 2015JY0262) and the scientific research project of Neijiang Normal University (No. 16JC08).

Author information

Authors and Affiliations

  1. Conservation and Utilization of Fishes resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Life sciences, Neijiang Normal University, Neijiang, 641100, Sichuan, China

    Yuan-Chao Zou, Bi-Wen Xie, Chuan-Jie Qin, Yong-Ming Wang, Deng-Yue Yuan, Rui Li & Zheng-Yong Wen

  2. School of Life Sciences, Southwest University, Chongqing, 400700, China

    Yuan-Chao Zou

Authors
  1. Yuan-Chao Zou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bi-Wen Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chuan-Jie Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yong-Ming Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Deng-Yue Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rui Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zheng-Yong Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yuan-Chao Zou or Zheng-Yong Wen.

Ethics declarations

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human subjects by any of the authors. The animal experiment throughout the study was conducted according to the Chinese Ministry of Science and Technology Guiding Directives for Humane Treatment of Laboratory Animals.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 125 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zou, YC., Xie, BW., Qin, CJ. et al. The complete mitochondrial genome of a threatened loach (Sinibotia reevesae) and its phylogeny. Genes Genom 39, 767–778 (2017). https://doi.org/10.1007/s13258-017-0541-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-017-0541-8

Keywords

Search

Navigation