RESUMO
Turnix suscitator (barred-button quail) is a member of the primitive genus Turnix in the highly diverse order of shore birds Charadriiformes. Absence of genome scale data of T. suscitator has limited our understanding about its systematics, taxonomic and evolutionary history as well has hindered the characterization of genome wide microsatellite markers of the same. Hence we generated whole genome short read sequences of T. suscitator, created a high quality assembly and mined genome-wide microsatellite markers from the same. A total of 34142524 reads were sequenced with an estimated genome size of 817 mb. SPAdes assembly consisted of 320761 total contigs and an estimated N50 value of 907 base pairs. Krait identified a total of 77028 microsatellite motifs covering 0.64% of the total sequences in the SPAdes assembly. Further the whole genome sequence and genome wide microsatellites dataset of T. suscitator will facilitate future genomic/evolutionary studies of Turnix species.
RESUMO
Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species 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 and scientific basis for phylogenetic revision of the genus Psittacula.
Assuntos
Genoma Mitocondrial/genética , Mitocôndrias/genética , Mitógenos/genética , Psittacula/genética , Animais , Uso do Códon/genética , Ordem dos Genes/genética , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética , Seleção Genética/genéticaRESUMO
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.
