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The mitochondrial genome of pin-tailed snipe Gallinago stenura , and its implications for the phylogeny of Charadriiformes

View Article: PubMed Central - PubMed

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.

No MeSH data available.


The AT skew and GC skew in Charadriiformes mitogenomes.Each point represents a species.
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pone.0175244.g004: The AT skew and GC skew in Charadriiformes mitogenomes.Each point represents a species.

Mentions: AT and GC skews are a measure of compositional asymmetry. In Charadriiformes mitogenomes, AT skews values were always positive, while the values of GC skew were negative. The AT skew value observed is 0.12 ± 0.02 (mean ± SD), ranging from 0.09 (Sternula albifrons) to 0.15 (Recurvirostra avosetta). The GC skews value is −0.38 ± 0.01, ranging from −0.40 (Jacana spinose) to −0.36 (S. albifrons) (Table 2). The lowest value of GC skew was always found in Jacanidae (−0.40), and highest value was found in Laridae (−0.36 to −0.37). In general, AT and GC skews in Charadriiformes mitogenomes are similar to patterns typically found in most animal mitogenomes, which positive AT skew and negative GC skew are found for H-strand, implying the specific bias toward A and C in nucleotide composition [47, 48]. The GC skew in Charadriiformes mitogenomes revealed that the ATP8 containing significantly higher skews than other regions, and the positive GC skew was not found in this work. However, there was a marked negative AT skew in ND1 (11 species), COI (three species), ND3 (five species), ND4L (one species) and CR (four species) on the H-strand (Fig 4).


The mitochondrial genome of pin-tailed snipe Gallinago stenura , and its implications for the phylogeny of Charadriiformes
The AT skew and GC skew in Charadriiformes mitogenomes.Each point represents a species.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383286&req=5

pone.0175244.g004: The AT skew and GC skew in Charadriiformes mitogenomes.Each point represents a species.
Mentions: AT and GC skews are a measure of compositional asymmetry. In Charadriiformes mitogenomes, AT skews values were always positive, while the values of GC skew were negative. The AT skew value observed is 0.12 ± 0.02 (mean ± SD), ranging from 0.09 (Sternula albifrons) to 0.15 (Recurvirostra avosetta). The GC skews value is −0.38 ± 0.01, ranging from −0.40 (Jacana spinose) to −0.36 (S. albifrons) (Table 2). The lowest value of GC skew was always found in Jacanidae (−0.40), and highest value was found in Laridae (−0.36 to −0.37). In general, AT and GC skews in Charadriiformes mitogenomes are similar to patterns typically found in most animal mitogenomes, which positive AT skew and negative GC skew are found for H-strand, implying the specific bias toward A and C in nucleotide composition [47, 48]. The GC skew in Charadriiformes mitogenomes revealed that the ATP8 containing significantly higher skews than other regions, and the positive GC skew was not found in this work. However, there was a marked negative AT skew in ND1 (11 species), COI (three species), ND3 (five species), ND4L (one species) and CR (four species) on the H-strand (Fig 4).

View Article: PubMed Central - PubMed

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.

No MeSH data available.