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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 usage of start and stop codons in the 13 mitochondrial protein-coding genes of the order Charadriiformes.All genes are shown in the order of occurrence in the mitochondrial genome starting from ND1.
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pone.0175244.g006: The usage of start and stop codons in the 13 mitochondrial protein-coding genes of the order Charadriiformes.All genes are shown in the order of occurrence in the mitochondrial genome starting from ND1.

Mentions: Start and stop codons vary among the protein-coding genes in Charadriiformes, although ATG and TAA were the most commonly observed. Start and stop codon usage biases were shown in Fig 6. Five start codons (ATG, GTG, ATT, ATC, and ATA) were detected in the 13 protein-coding genes. The most common start codon was ATG, which accounts for 78.85% of the start codons, followed by GTG (11.15%). The start codon ATG appeared in 12 protein-coding genes (with the exception of ND3), and 8 genes (COII, ATP8, ATP6, COIII, ND4L, ND4, Cyt b, and ND6) only used ATG as start codon. The start codon GTG was commonly used in the COI and ND5. Then the start codons ATT and ATC were only used in the ND3. The start codon ATA were found in the ND1, ND2, and ND3 (Fig 6), which was frequently observed in other avian orders [20]. While in the suborder Lari, the start codons ATC and ATA were not common used, as they were only found in the ND3 of S. antiquus and A. interpres [10].


The mitochondrial genome of pin-tailed snipe Gallinago stenura , and its implications for the phylogeny of Charadriiformes
The usage of start and stop codons in the 13 mitochondrial protein-coding genes of the order Charadriiformes.All genes are shown in the order of occurrence in the mitochondrial genome starting from ND1.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0175244.g006: The usage of start and stop codons in the 13 mitochondrial protein-coding genes of the order Charadriiformes.All genes are shown in the order of occurrence in the mitochondrial genome starting from ND1.
Mentions: Start and stop codons vary among the protein-coding genes in Charadriiformes, although ATG and TAA were the most commonly observed. Start and stop codon usage biases were shown in Fig 6. Five start codons (ATG, GTG, ATT, ATC, and ATA) were detected in the 13 protein-coding genes. The most common start codon was ATG, which accounts for 78.85% of the start codons, followed by GTG (11.15%). The start codon ATG appeared in 12 protein-coding genes (with the exception of ND3), and 8 genes (COII, ATP8, ATP6, COIII, ND4L, ND4, Cyt b, and ND6) only used ATG as start codon. The start codon GTG was commonly used in the COI and ND5. Then the start codons ATT and ATC were only used in the ND3. The start codon ATA were found in the ND1, ND2, and ND3 (Fig 6), which was frequently observed in other avian orders [20]. While in the suborder Lari, the start codons ATC and ATA were not common used, as they were only found in the ND3 of S. antiquus and A. interpres [10].

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.