Abstract
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.
Highlights
The mitochondrion, descended from an alpha-proteobacterium, is one of the fundamental eukaryotic organelles [1,2,3] and retains a remnant, bacterial-like genome
Quality control of the hand alignments was performed by comparing with homologous sequences from previously sequenced Cyclorrhapha mt genomes to identify several tRNAs apparently absent from the N. mamaevi mt genome, and to verify protein-coding genes (PCGs) and rRNAs annotations
Mt genome length is mediumsized when compared to the mt genomes of other Diptera, that range from 14,922 bp (Sarcophaga peregrine, Sarcophagidae, NC_023794) to 19,517 bp (Drosophila melanogaster, Drosophilidae [26])
Summary
The mitochondrion (mt), descended from an alpha-proteobacterium, is one of the fundamental eukaryotic organelles [1,2,3] and retains a remnant, bacterial-like genome. We re-annotated the mt genomes of all Cyclorrhapha species deposited on GenBank, based on comparative analysis of homologous genes, and undertook a statistical analysis of start and stop codons positions in their PCGs. We aligned and analysed two intergenic sequences across Cyclorrapha, which were highly conserved 18-bp motifs for the binding site of mtTERM.
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