Abstract
Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
Highlights
Aves are one of the most diverse vertebrate classes with a huge number of species having a broad range of ecological behavior and complex morphology, all of which make it difficult to solve the riddles regarding their taxonomy along with phylogenetic and evolutionary r elationship[1,2,3]
We report for the first time the complete mitogenome of Turdoides affinis (MN848144)
Our results suggested that the de-novo assembly approach is more appropriate than a reference-based assembly approach
Summary
Aves are one of the most diverse vertebrate classes with a huge number of species having a broad range of ecological behavior and complex morphology, all of which make it difficult to solve the riddles regarding their taxonomy along with phylogenetic and evolutionary r elationship[1,2,3]. It has been reported that complete mitogenomes retain more information than a single gene regarding the evolutionary history of the taxon and provide consistent results compared to nuclear genes[11]. This reduces the effect of homoplasy and frequent stochastic errors in phylogenetic studies[11]. Leiothrichidae, Pellorneidae and Timaliidae consisted of traditional babblers while Zosteropidae that included mainly Yuhina and some other minor species, and Sylviidae grouped all the Sylvia warblers[14]. We have performed a detailed comparative analysis of mitogenomes of the available members from family Leiothrichidae to understand the overall species-specific differences
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