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

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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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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

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