Dataset Information

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

ABSTRACT: In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes CO? and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the T?C arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.

SUBMITTER: Ma YG

PROVIDER: S-EPMC5042932 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

Ma Yong-Gui YG Huang Yuan Y Lei Fu-Min FM

Dong wu xue yan jiu = Zoological research 20140301 2

In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop cod ...[more]

PMID: 24668650

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Project description:Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.

Dataset Information

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

Publications

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

Similar Datasets

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