Abstract
Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNA Ser(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNA Ile has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.
Highlights
The mitochondrion is an important organelle in eukaryotic cells
The genome is mediumsized in compared with other Diptera mitochondrial genomes that range from 14,503 bp (Rhopalomyia pomum) to 19,517 bp (Drosophila melanogaster) in length
The study suggest that both Oestroidea and Muscoidea are polyphyletic, which are partially supported by Kutty et al (2008) and Nelson et al (2012) [15, 17]. This is the first report of complete mitochondrial genome of the family Anthomyiidae
Summary
The mitochondrion is an important organelle in eukaryotic cells. It is connected with energy metabolism, apoptosis, aging, and disease and is a location for oxidative phosphorylation [1]. The mitochondrial genome is a covalently closed circular double-stranded molecule with a small molecular weight. It has a high copy number, does not contain introns, has a compact gene arrangement, and is lack of recombination [3]. The noncoding A+T rich region, called as the control region (CR), is considered to control the replication and transcription of the mitochondrial genome [4]. The length variation among insect mitochondrial genomes is mainly determined by variation in the A+T rich region, which varies from 70 to 13 kb in length [5]
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