title: The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes.
abstract: The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.
authors.affiliation: Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Chaochao
authors.initials: C
authors.lastname: Hu
authors.affiliation: Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Chenling
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, United States of America.
authors.forename: Lei
authors.initials: L
authors.lastname: Sun
authors.affiliation: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Wenli
authors.initials: W
authors.lastname: Xie
authors.affiliation: Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui, People's Republic of China.
authors.forename: Baowei
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
authors.forename: Qing
authors.identifier: http://orcid.org/0000-0003-1057-4393
authors.initials: Q
authors.lastname: Chang
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D046091:Charadriiformes / Q000235:genetics*; D018387:Codon, Initiator; D018388:Codon, Terminator; D054629:Genome, Mitochondrial; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012343:RNA, Transfer / Q000737:chemistry
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator; D012343:RNA, Transfer