The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

Yoon, Kwang Bae; Cho, Chea Un; Park, Yung Chul

doi:10.1016/j.gene.2015.07.022

Cited by 6 publications

(8 citation statements)

References 61 publications

(82 reference statements)

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“…The completely sequenced mitogenomes from Charadriiformes encode a CR, and a typical set of 37 mitochondrial genes containing 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), and 22 tRNA genes. Gene arrangement is highly conserved within the Charadriiformes mitogenomes, without showing any structural rearrangement [10, 14]. The gene of ND6 and 8 tRNA are encoded on the light strand, whereas the other genes are located on the heavy strand (S2 Table).…”

Section: Resultsmentioning

confidence: 99%

“…In the species of C . saundersi , Yoon et al (2015) found the extra base in ND3, whereas Ryu and Kwang (2012) lacked it [10, 52]. The extra base insert in ND3 has been observed in some birds and turtles [53], but it appears to be randomly happened in closely related species, even within species [10, 52].…”

Section: Resultsmentioning

confidence: 99%

“…Twenty-two tRNA genes were identified in Charadriiformes in the same genomic positions as observed in Laridae [10], with an average size ranging from 65.0 ± 0.9 bp in tRNA Ser (AGY) to 74.0 ± 0.2 bp in tRNA Leu (UUR) . The length difference was due to the mutation of stem and loop sizes of the dihydrouridine (DHU) and TΨC arms.…”

Section: Resultsmentioning

confidence: 99%

“…The two aligned datasets were 13,965 and 10,773 bp in length for the Dataset 1 and Dataset 2 matrices, respectively. In all phylogenetic analyses, Columba livia , Gallus gallusa , Phodilus badius , and Zenaida auriculata were used as outgroups [10, 12, 42, 43]. Before reconstructing the phylogenetic trees, sequence alignment was carried out.…”

Section: Methodsmentioning

confidence: 99%

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

Zhang

Sun

et al. 2017

PLoS ONE

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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 () and 7 bp () 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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

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

Zhang

Sun

et al. 2017

PLoS ONE

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“…Nos bancos de dados internacionais de sequências genéticas (GeneBank, EMBL, PDB, etc. ), a maioria das sequências de aves marinhas depositadas são provenientes de trabalhos de cunho filogenético, principalmente os de grandes grupos (Hedges & Sibley, 1994;Stanley & Harrison, 1999;Shapiro & Dumbacher, 2001;Moum et al, 2002;Paton et al, 2003;Austin et al, 2004;Bridge et al, 2005;Baker et al, 2007;Yoon et al, 2015;Hu et al, 2017).…”

Section: Estudos Genéticos Em Aves Marinhasunclassified

Taxonomia e biogeografia de Rynchops niger (Rynchopinae) e Phaetusa simplex (Sterninae) (Aves, Charadriiformes): utilizando a morfologia e marcadores moleculares para investigar a estrutura populacional e o papel dos rios na evolução e migração de aves aquáticas

Gouvêa¹

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Porque eu entendo, desde a minha pobre percepção, que o vencedor, no fim das contas, é aquele que atinge o inútil dos pássaros e dos lírios do campo. Ah, que estas palavras gratuitas possam agora servir de abrigo para todos os pássaros do mundo." Manoel de Barros Gratuidade das Aves e dos Lírios Agradecimentos Esta foi uma jornada longa, com doses de ansiedade e muitas pitadas de alegria. Uma jornada de muito aprendizado pela qual eu sou muito grata e de que de forma alguma poderia se concretizar sem a ajuda de uma série de pessoas. Você pode até escrever poesia sozinho(a), mas ciência, meu caro, é impossível fazer só. Desta forma, eu gostaria de agradecer: Ao meu querido orientador e amigo Prof. Dr. Luís Fábio Silveira, por abrir as portas da ornitologia, acreditar em mim e me dar todo o apoio necessário. Além do bom humor, que fizeram toda a diferença e tornaram esta caminhada muito mais tranquila e agradável. Ao amigo e coorientador Dr. Gustavo Bravo, que me incentivou e guiou "no mundo da biologia molecular". Gratidão pela orientação e ajuda concreta durante todo o período em que estive em Harvard. Ao CNPQ (Conselho Nacional de Desenvolvimento Científico e Tecnológico) pela concessão da bolsa de doutorado e à CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) pela bolsa de PDSE (Programa de Doutorado-sanduíche no Exterior), ambas imprescindíveis para a realização deste trabalho.

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

et al. 2018

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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.

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The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

Cited by 6 publications

References 61 publications

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

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

Taxonomia e biogeografia de Rynchops niger (Rynchopinae) e Phaetusa simplex (Sterninae) (Aves, Charadriiformes): utilizando a morfologia e marcadores moleculares para investigar a estrutura populacional e o papel dos rios na evolução e migração de aves aquáticas

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

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