Complete mitochondrial genome of the Siberian thrush,Geokichla sibirica sibirica(Aves, Turdidae)

Sun, Cheng‐He; Liu, Bin; Lu, Changhu

doi:10.1080/23802359.2019.1591195

Cited by 15 publications

(3 citation statements)

References 7 publications

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“…The tRNAscan-SE v2.0 ( Lowe and Chan, 2016 ) software and MITOS WebServer 1 ( Bernt et al, 2013 ) were used to verify the tRNA genes. Open reading frame finder ( Master et al, 2016 ; Sun et al, 2019b ) and the NCBI website were used to identify the protein-coding regions by using the default settings for the vertebrate mitochondrial code, and GenBank was used to translate the putative proteins. The sequences of the identified PCGs and rRNAs were analyzed and compared with those of other Characidae species.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

Sun

Liu

et al. 2021

Front. Genet.

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The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T−−/TA−. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.

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Section: Methodsmentioning

confidence: 99%

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

Sun

Liu

et al. 2021

Front. Genet.

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“…The mitogenome of E. zantholeuca is similar to other birds: it is a double-stranded circular mol-ecule composed of 37 typical genes and a control region. Meanwhile, there are also intergenic spacers and overlaps between genes, as is seen in other birds [Krajewski et al, 2010;Master et al, 2016;Dong et al, 2018;Sun et al, 2019]. The gene order of the mitogenome analyzed is highly conserved and is also identical to the gene order found in the mitogenome of Gallus gallus [Dejardins and Morais, 1990].…”

Section: Mitogenome Characteristicsmentioning

confidence: 77%

The New Mitogenome of Erpornis zantholeuca (Aves: Passeriformes): Sequence, Structure, and Phylogenetic Analyses

Yuan

Sha

Duan

2022

Cytogenet Genome Res

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White-bellied Erpornis (Erpornis zantholeuca) is a group of birds in the order Passeriformes, but its taxonomic status remains controversial. To understand the phylogenetic position of E. zantholeuca and phylogenetic relations within this family, we sequenced the complete mitochondrial genome of E. zantholeuca, which was 16,902 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the whole genome was 30.10% A, 30.48% C, 15.14% G, and 24.28% T and showed an elevated AT content (54.38%). All genes were encoded on the H-strand, with the exceptions of 8 tRNAs (trnQ, trnA, trnN, trnC, trnY, trnS2(UCN), trnP, trnE) and 1 PCG (Mt-ND6). Most PCGs used standard ATN as start codons, and TAN as stop codons. All tRNAs were predicted to form the typical cloverleaf secondary structures. The gene order of E. zantholeuca was consistent with that of Gallus gallus, which was considered to be a plesiomorphic or typical avian gene order. Phylogenetic relationships based on bayesian inference and maximum likelihood methods showed that E. zantholeuca was well supported as the sister group of (Vireo altiloquus + Vireo olivaceus). In addition, Pteruthius melanotis was sister to the other members of Vireonidae.

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“… 2019 ; Sun et al. 2019 ). The structure of the mitogenome is a typical vertebrate mitochondrial gene arrangement.…”

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confidence: 99%

The complete mitochondrial genome of red-throated flycatcher Ficedula albicilla (Passeriformes: Ficedula)

Zhang

2019

Mitochondrial DNA Part B

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We report the mitochondrial genome of Ficedula albicilla. The overall base composition of F. albicilla mitogenome is 29.49%A, 15.06%G, 32.98%C, and 22.47%T, with an A þ T content of 51.96%. The total length of the sequence is 16,791 bp (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control regions). Phylogenetic analysis was performed based on the concatenated nucleotide sequences of cytochrome c oxidase subunit I and cytochrome b using the neighbor-joining method and the Kimura 2-parameter model in MEGA 7.0 with 1000 bootstrap replicates.

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Complete mitochondrial genome of the Siberian thrush,Geokichla sibirica sibirica(Aves, Turdidae)

Cited by 15 publications

References 7 publications

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

The New Mitogenome of Erpornis zantholeuca (Aves: Passeriformes): Sequence, Structure, and Phylogenetic Analyses

The complete mitochondrial genome of red-throated flycatcher Ficedula albicilla (Passeriformes: Ficedula)

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