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The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii

Abstract

The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii’s mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.

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Acknowledgements

We wish to thank Peng Chen for kindly collecting samples, Yunhao Wu and Deyun Tai for data analysis, and Yi Zhang for the help with laboratory work. This research was supported by Grants from the Natural Science Research Program of Jiangsu Higher Education Institutions of China (Grant Nos. 16KJB180003, 16KJB180012); ‘12th Five-Year’ Planning Issue of Jiangsu Open University (The City Vocational College of Jiangsu) (Grant No. 15SEW-Y-018); Training program of innovation and entrepreneurship for undergraduates in Jiangsu, China (Grant No. 201714000015X); and Nature Science Fund of Jiangsu Province (Grant No. BK20161480).

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Correspondence to Chaochao Hu.

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Chen, W., Zhang, C., Pan, T. et al. The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii. Genes Genom 40, 955–963 (2018). https://doi.org/10.1007/s13258-018-0703-3

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Keywords

  • Mitogenome
  • Charadrii
  • Charadrius alexandrinus
  • Phylogeny