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The complete mitochondrial genome of the Thick-billed Flowerpecker (Dicaeum agile).

ABSTRACT: The Thick-billed Flowerpecker (Dicaeum agile), a small member of the flowerpecker family, inhabits tropical Southern Asia, and is widely distributed from India east to Indonesia and Timor. In this study, next generation sequencing (NGS) was used to obtain a mitochondrial genome sequence for D. agile. The complete mitogenome was 16,809bp in length, with a GC content of 46.40%. The genome sequence contained thirteen protein-coding genes, one 12S RNA gene, one 16S RNA gene, and 22 tRNA genes. A phylogenetic tree constructed for the family confirmed that D. agile is closely related to another species of Dicaeum (Dicaeum eximium). The mitochondrial genome of the Thick-billed Flowerpecker will be useful for future phylogeographic studies of this species.

SUBMITTER: Gao Y

PROVIDER: S-EPMC8143603 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The complete sequence of honeybee (Apis mellifera) mitochondrial DNA is reported being 16,343 bp long in the strain sequenced. Relative to their positions in the Drosophila map, 11 of the tRNA genes are in altered positions, but the other genes and regions are in the same relative positions. Comparisons of the predicted protein sequences indicate that the honeybee mitochondrial genetic code is the same as that for Drosophila; but the anticodons of two tRNAs differ between these two insects. The base composition shows extreme bias, being 84.9% AT (cf. 78.6% in Drosophila yakuba). In protein-encoding genes, the AT bias is strongest at the third codon positions (which in some cases lack guanines altogether), and least in second codon positions. Multiple stepwise regression analysis of the predicted products of the protein-encoding genes shows a significant association between the numbers of occurrences of amino acids and %T in codon family, but not with the number of codons per codon family or other parameters associated with codon family base composition. Differences in amino acid abundances are apparent between the predicted Apis and Drosophila proteins, with a relative abundance in the Apis proteins of lysine and a relative deficiency of alanine. Drosophila alanine residues are as often replaced by serine as conserved in Apis. The differences in abundances between Drosophila and Apis are associated with %AT in the codon families, and the degree of divergence in amino acid composition between proteins correlates with the divergence in %AT at the second codon positions. Overall, transversions are about twice as abundant as transitions when comparing Drosophila and Apis protein-encoding genes, but this ratio varies between codon positions. Marked excesses of transitions over chance expectation are seen for the third positions of protein-coding genes and for the gene for the small subunit of ribosomal RNA. For the third codon positions the excess of transitions is adequately explained as due to the restriction of observable substitutions to transitions for conserved amino acids with two-codon families; the excess of transitions over expectation for the small ribosomal subunit suggests that the conservation of nucleotide size is favored by selection.

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The complete mitochondrial genome of the Thick-billed Flowerpecker (Dicaeum agile).

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