Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses

Sun, Cheng‐He; Liu, Hongyi; Lu, Changhu

doi:10.1016/j.ijbiomac.2019.12.253

Cited by 23 publications

(18 citation statements)

References 61 publications

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“…The overall A-T and G-C skew were 0.1800 and -0.4259, respectively (Table 3), indicating higher A nucleotide than T nucleotide, and higher C nucleotide than G nucleotide, respectively. The A-T and G-C skew values also indicated that Psittacula species are having higher A and C content than T and G as reported earlier in certain other birds [29,50]. (Table 4).…”

Section: Resultssupporting

confidence: 77%

“…Heat-maps based on codon usage ( respectively, similar to the nucleotide contents of the P. cyanocephala rRNAs. Birds are generally characterized by similar positioning of and high A+T content in their rRNAs, reported across many avian orders [50,53]. As such the rRNAs of the Psittacula species compared in this study displayed similar positioning and characteristics of rRNAs typical of avian orders.…”

Section: Protein-coding Genessupporting

confidence: 51%

“…including the members of Psittaciformes order and certain other birds [29,50,51]. The overall A-T and G-C skew were 0.1800 and -0.4259, respectively (Table 3), indicating higher A nucleotide than T nucleotide, and higher C nucleotide than G nucleotide, respectively.…”

Section: Resultsmentioning

confidence: 99%

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Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis

Dey¹,

Sharma²,

Sarkar³

et al. 2020

Preprint

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Psittacula cyanocephala is a parakeet endemic to the Indian sub-continent, widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting further studies to resolve such issues. Since the mitochondrial genome provides useful information about a species concerning its evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species, scientific basis for phylogenetic revision of genus Psittacula.

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Section: Resultssupporting

confidence: 77%

Section: Protein-coding Genessupporting

confidence: 51%

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Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis

Dey¹,

Sharma²,

Sarkar³

et al. 2020

Preprint

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“…The nucleotide composition of the complete mitogenome was as follows: A ¼ 4905 (29.26%), T ¼ 3909 (23.32%), G ¼ 2496 (14.89%), C ¼ 5451 (32.52%). The entire mitogenome had a high A þ T content of 52.59%, including 51.52% in PCGs, 57.05% in tRNA genes, 54.02% in rRNA genes, and 54.65% in the D-loop, concurrent with the typical base bias of avian mitogenomes (Haring et al 2001;Bi et al 2019;Liu et al 2019;Sun et al 2019aSun et al , 2019b.…”

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confidence: 99%

Complete mitochondrial genome of the Grey thrush Turdus cardis (Aves, Turdidae)

Sun

et al. 2020

Mitochondrial DNA Part B

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The mitogenome was sequenced through whole-genome shotgun sequencing using the Illumina platform, and phylogenetic analysis was carried out on the basis of 13 PCGs and two rRNAs. The complete T. cardis mitogenome comprised 16,761 bp, MN865118. The organization and location of genes in the T. cardis mitogenome were consistent with those reported for other Turdidae species. Phylogenetic relationships based on Bayesian inference and the Maximum likelihood method revealed that T. cardis was closely related to Turdus hortulorum, indicating that the molecular taxonomy of T. cardis is consistent with its current morphological characteristics. Our mitogenomic data may have applications in further phylogenetic and taxonomic studies of Turdidae. ARTICLE HISTORY

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“…Calidris pugnax mitogenome can contribute to our understanding of the phylogeny and evolution of this species. (Boore 1999;Sun et al 2020).…”

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confidence: 99%

Complete mitochondrial genome of the Ruff, Calidris pugnax(Aves, Scolopacidae)

Chen

Zhang

Wang

et al. 2020

Mitochondrial DNA Part B

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This paper reports the mitochondrial genome of Calidris pugnax, which is a closed circular molecule of 16,902 bp. The overall base composition of this species is 25.2% T, 30.6% C, 32.0% A, and 12.2% G, with an A þ T content of 55.2%. The structure of the mitogenome is a typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis of complete mitochondrial genome concatenated sequences from 13 species from 6 genera was conducted using the maximum-likelihood (ML) model. The topology demonstrated that the mitogenome of this species was genetically closest to that of Calidris tenuirostris. Calidris pugnax mitogenome can contribute to our understanding of the phylogeny and evolution of this species.

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Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses

Cited by 23 publications

References 61 publications

Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis

Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis

Complete mitochondrial genome of the Grey thrush Turdus cardis (Aves, Turdidae)

Complete mitochondrial genome of the Ruff, Calidris pugnax(Aves, Scolopacidae)

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