Dataset Information

Complete mitochondrial genome of the isabelline wheatear Oenanthe isabellina (Passeriformes, Muscicapidae).

ABSTRACT: The isabelline wheatear Oenanthe isabellina was widespread in Northern Hemisphere, but the information of this species is poorly known. In this study, the complete sequence of O. isabellina mitochondrial genome was obtained by L-PCR and conserved primer-walking approaches. The results showed that the entire mitochondrial genome of O. isabellina was 16,812?bp in length with 52.7% A?+?T content; the genome harbored the same gene order as that of other birds, including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop). All protein-coding genes of O. isabellina mitochondrial genome started with an ATG codon, except for COI with GTG. For terminate codon usage, most of the genes use TAA or TAG. The control region of O. isabellina was located between tRNA-Glu and tRNA-Phe with 1244?bp length, no repetitive sequence. The mitochondrial data are potentially important for understanding this poorly known species.

SUBMITTER: Li S

PROVIDER: S-EPMC7800959 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Publications

Complete mitochondrial genome of the isabelline wheatear Oenanthe isabellina (Passeriformes, Muscicapidae).

Li Shaobin S Luo An A Li Guopan G Li Wei W

Mitochondrial DNA. Part B, Resources 20160620 1

The isabelline wheatear Oenanthe isabellina was widespread in Northern Hemisphere, but the information of this species is poorly known. In this study, the complete sequence of O. isabellina mitochondrial genome was obtained by L-PCR and conserved primer-walking approaches. The results showed that the entire mitochondrial genome of O. isabellina was 16,812 bp in length with 52.7% A + T content; the genome harbored the same gene order as that of other birds, including 2 rRNA g ...[more]

PMID: 33473481

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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.

Project description:We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almost doubled their lean body mass. The sample structure used to build up the transcriptome of the Northern Wheatears concerning tissue composition and time guarantees the future survey of the regulatory genes involved in the development of the migratory phenotype. Through the pre-migratory period, birds accomplish outstanding physical and behavioural changes that involve all organ systems. Nevertheless, the molecular mechanisms through which birds synchronize and control hyperphagia, fattening, restlessness increase, immunity boosting and tuning the muscles for such endurance flight are still largely unknown. The use of RNA-Seq has emerged as a powerful tool to analyse complex traits on a broad scale, and we believe it can help to characterize the migratory phenotype of wheatears at an unprecedented level. The primary challenge to conduct quantitative transcriptomic studies in non-model species is the availability of a reference transcriptome, which we have constructed and described in this paper. The cDNA was sequenced by pyrosequencing using the Genome Sequencer Roche GS FLX System; with single paired-end reads of about 400 bp. We estimate the total number of genes at 15,640, of which 67% could be annotated using Turkey and Zebra Finch genomes, or protein sequence information from SwissProt and NCBI databases. With our study, we have made a first step towards understanding the migratory phenotype regarding gene expression of a species that has become a model to study birds long-distance migrations.

Dataset Information

Complete mitochondrial genome of the isabelline wheatear Oenanthe isabellina (Passeriformes, Muscicapidae).

Publications

Complete mitochondrial genome of the isabelline wheatear <i>Oenanthe isabellina</i> (Passeriformes, Muscicapidae).

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