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The mitochondrial genome of red-necked phalarope Phalaropus lobatus (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae

Genes & Genomics volume 40, pages 455–463 (2018)Cite this article

Abstract

The red-necked phalarope is a wonderful species with specific morphological characters and lifestyles. Mitochondrial genomes, encoding necessary proteins involved in the system of energy metabolism, are important for the evolution and adaption of species. In this study, we determined the complete mitogenome sequence of Phalaropus lobatus (Charadriiformes: Scolopacidae). The circular genome is 16714 bp in size, containing 13 PCGs, two ribosomal RNAs and 22 tRNAs and a high AT-rich control region. The AT skew and GC skew of major strand is positive and negative respectively. Most of PCGs are biased towards A-rich except ND1. A codon usage analysis shows that 3 start codons (ATG, GTG and ATA), 4 stop codons (TAA, TAG, AGG, AGA) and two incomplete terminate codons (T–). Twenty two transfer RNAs have the typical cloverleaf structure, and a total of ten base pairs are mismatched throughout the nine tRNA genes. The phylogenetic tree based on 13 PCGs and 2 rRNA genes indicates that monophyly of the family and genus Phalaropus is close to genus Xenus plus Tringa. The analysis of selective pressure shows 13 protein-coding genes are evolving under the purifying selection and P. lobatus is different from other Scolopacidae species on the selective pressure of gene ND4. This study helps us know the inherent mechanism of mitochondrial structure and natural selection.

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References

  • Anderson S, Bankier AT, Barrell BG, De Bruijin MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F et al (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465

    Article  CAS  PubMed  Google Scholar 

  • Baker AJ, Pereira SL, Paton TA (2007) Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol Lett 3:205–210

    Article  PubMed  PubMed Central  Google Scholar 

  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–319

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brown RGB, Gaskin DE (1988) The pelagic ecology of the Grey and Red-necked Phalaropes Phalaropus fulicarius and P. lobatus in the Bay of Fundy, eastern Canada. Ibis 130:234–250

    Article  Google Scholar 

  • Gibson R, Baker A (2012) Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes). Mol Phylogenet Evol 64:66–72

    Article  PubMed  Google Scholar 

  • Giroux MA, Ditlecadet D, Martin LJ, Lanctot RB, Lecomte N (2016) Sexing a sex-role-reversed species based on plumage: potential challenges in the red phalarope. Peer J 4:e1989

    Article  PubMed  PubMed Central  Google Scholar 

  • Hirst J (2005) Energy transduction by respiratory complex I—an evaluation of current knowledge. Biochem Soc Trans 33:525–529

    Article  CAS  PubMed  Google Scholar 

  • Hu C, Zhang C, Sun L, Zhang Y, Xie W, Zhang B, Chang Q (2017) The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes. PLoS ONE 12:e0175244

    Article  PubMed  PubMed Central  Google Scholar 

  • Huntley B, Collingham YC, Willis SG, Green RE (2008) Potential impacts of climatic change on european breeding birds. PLoS ONE 3:e1439

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:msw054

    Google Scholar 

  • Lavrov DV, Boore JL, Brown WM (2002) Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol Biol Evol 19:163–169

    Article  CAS  PubMed  Google Scholar 

  • Lehninger AL (1970) Mitochondria and calcium ion transport. Biochem J 119:129–138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lowe TM, Eddy SRB (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 

  • Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA (2011) Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol 28:1927–1942

    Article  CAS  PubMed  PubMed Central  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 

  • Peter H, Fain MG (2007) Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves). BMC Evol Biol 7:35

    Article  Google Scholar 

  • Uddin A, Choudhury MN, Chakraborty S (2016) Codon usage bias and phylogenetic analysis of mitochondrial ND1 gene in pisces, aves, and mammals. Mitochondrial DNA Part A 1:1–13

    Article  Google Scholar 

  • Varani G, McClain WH (2000) The G· U wobble base pair. EMBO Rep 1:18–23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Verkuil YI, Piersma T, Baker AJ (2010) A novel mitochondrial gene order in shorebirds (Scolopacidae, Charadriiformes). Mol Phylogenet Evol 57:411–416

    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 

  • Yang Z (2007) Paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang QL, Zhang L, Zhao TX, Wang J, Zhu QH, Chen JY, Yuan ML (2017) Gene sequence variations and expression patterns of mitochondrial genes are associated with the adaptive evolution of two Gynaephora species (Lepidoptera: Lymantriinae) living in different high-elevation environments. Gene 610:148–155

    Article  CAS  PubMed  Google Scholar 

  • Zou Z, Min Q, Cheng S, Xin T, Xia B (2017) The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae), a host insect of Ophiocordyceps sinensis and its implication in taxonomic revision of Hepialus adopted in China. Gene 601:44–55

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by grants from the Program of National Natural Science Foundation of China (#31071901 and #41271057), Natural Science Research Program of Jiangsu Higher Education Institutions of China (#15KJD180005 and #16KJB180012) and Postgraduate Research & Practice Innovation Program of Jiangsu Province (#KYCX17_1073).

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Authors and Affiliations

  1. Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1# Wenyuan Road, Nanjing, 210023, Jiangsu, People’s Republic of China

    Wei Liu, Wenli Xie, Peng Chen, Yi Zhang, Ran Yao, Kexin Li & Qing Chang

  2. Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People’s Republic of China

    Chaochao Hu

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  1. Wei Liu
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  2. Chaochao Hu
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  3. Wenli Xie
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  4. Peng Chen
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  5. Yi Zhang
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  6. Ran Yao
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  7. Kexin Li
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  8. Qing Chang
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Corresponding author

Correspondence to Qing Chang.

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Conflict of interest

Wei Liu declares that he has no conflict of interest. Chao–Chao Hu declares that he has no conflict of interest. Wen-Li Xie declares that she has no conflict of interest. Peng Chen declares that he has no conflict of interest. Yi Zhang declares that she has no conflict of interest. Ran Yao declares that she has no conflict of interest. Ke-Xin Li declares that she has no conflict of interest. Qing Chang declares that he has no conflict of interest.

Ethical approval

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.

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Liu, W., Hu, C., Xie, W. et al. The mitochondrial genome of red-necked phalarope Phalaropus lobatus (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae. Genes Genom 40, 455–463 (2018). https://doi.org/10.1007/s13258-017-0632-6

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  • DOI: https://doi.org/10.1007/s13258-017-0632-6

Keywords

  • Mitogenome
  • Red-necked phalarope
  • Evolution
  • Phylogeny