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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.


Organization of the control region in Charadriiformes mitochondrial genomes.The location and copy number of tandem repeats are shown by oval with Arabic numerals inside. Non-repeat regions are indicated by square box. L: Length.
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pone.0175244.g007: Organization of the control region in Charadriiformes mitochondrial genomes.The location and copy number of tandem repeats are shown by oval with Arabic numerals inside. Non-repeat regions are indicated by square box. L: Length.

Mentions: We observed large tandem repeats with two or more copies in CR with the exception of I. relictus. In most species (12/20), tandem repeat sequences only had one type of repeat unit. Tandem repeat sequences contained two types of repeat units in 5 species (V. vanellus; C. brunnicephalus, C. ridibundus, C. saundersi, and L. dominicanus). The sequences contained three and four types in Jacana spinosa and J. jacana respectively (Fig 7). Total of 15 kinds of tandem repeats were found in CR. The motifs of 5’-AAACAAC-3’ (occurs in 7 species) and 5’-AAAC-3’ (in 5 species) are most common. However, 10/15 motifs were only found in one species, suggesting the fast rate evolution in the CR. Two long motifs of n (79 nucleotides with 2 tandem repeats) and o (82 nucleotides with 5 tandem repeats) only occurred in Jacava (Fig 7). Interestingly, the five motifs (a, c, f, l and m) had large copies (Fig 7), which had a strictly conserved common sequence (5’-AAAC-3’). The CR of Charadriiformes mitogenome shows distinct sequence and structural characteristics, such as varying sizes and diverse tandem repeats, which are taxon-specific and can potentially be used as genetic markers for evolution and population genetic studies.


The mitochondrial genome of pin-tailed snipe Gallinago stenura , and its implications for the phylogeny of Charadriiformes
Organization of the control region in Charadriiformes mitochondrial genomes.The location and copy number of tandem repeats are shown by oval with Arabic numerals inside. Non-repeat regions are indicated by square box. L: Length.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0175244.g007: Organization of the control region in Charadriiformes mitochondrial genomes.The location and copy number of tandem repeats are shown by oval with Arabic numerals inside. Non-repeat regions are indicated by square box. L: Length.
Mentions: We observed large tandem repeats with two or more copies in CR with the exception of I. relictus. In most species (12/20), tandem repeat sequences only had one type of repeat unit. Tandem repeat sequences contained two types of repeat units in 5 species (V. vanellus; C. brunnicephalus, C. ridibundus, C. saundersi, and L. dominicanus). The sequences contained three and four types in Jacana spinosa and J. jacana respectively (Fig 7). Total of 15 kinds of tandem repeats were found in CR. The motifs of 5’-AAACAAC-3’ (occurs in 7 species) and 5’-AAAC-3’ (in 5 species) are most common. However, 10/15 motifs were only found in one species, suggesting the fast rate evolution in the CR. Two long motifs of n (79 nucleotides with 2 tandem repeats) and o (82 nucleotides with 5 tandem repeats) only occurred in Jacava (Fig 7). Interestingly, the five motifs (a, c, f, l and m) had large copies (Fig 7), which had a strictly conserved common sequence (5’-AAAC-3’). The CR of Charadriiformes mitogenome shows distinct sequence and structural characteristics, such as varying sizes and diverse tandem repeats, which are taxon-specific and can potentially be used as genetic markers for evolution and population genetic studies.

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.