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

다국어 초록 (Multilingual 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.

번역하기

참고문헌 (Reference)

1 Lowe TM, "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence" 25 : 955-964, 1997

2 Mayr G, "The phylogeny of Charadriiform birds (shorebirds and allies): reassessing the conflict between morphology and molecules" 161 : 916-934, 2011

3 Yoon KB, "The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)" 572 : 227-236, 2015

4 Hu C, "The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes" 12 : e0175244-, 2017

5 Ren Q, "The complete mitochondrial genome of the yellowbrowed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae), and phylogenetic relationships within the genus Emberiza" 93 : 699-707, 2014

6 Smith NA, "Systematics and evolution of the Pan-Alcidae (Aves, Charadriiformes)" 46 : 125-140, 2015

7 Friesen VL, "Speciation in seabirds: why are there so many species... and why aren't there more?" 156 : 1-13, 2015

8 Paton TA, "Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree" 39 : 657-667, 2006

9 Paton TA, "RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds" 29 : 268-278, 2003

10 Hassanin A, "Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution" 38 : 100-116, 2006