Abstract: The study aims to investigate the structural characteristics of Diptera mitochondrial genomes and design universal primers for sequencing of Diptera mitochondrial genomes so as to establish an overall framework of information for further study of Diptera mitochondrial genomes. We analyzed the structural characteristics, base composition and conserved regions of dipteran mitochondrial genome based on the known 26 fulllength mitochondrial genome sequences of Diptera using comparative genomics and bioinformatics methods, and designed a set of universal primers for mitochondrial genome sequencing of Diptera. The results show that the mitochondrial genomes of Diptera are 14 503-19 517 bp in length, and their structure are quite conservative with 37 coding genes, including 13 protein-coding genes, 22 tRNA genes and two rRNA coding genes. In addition, there is a non-coding region (AT-rich region) with various lengths. The individual gene location order on these genomes is quite stable, consistent with that on the mitochondrial genome of Drosophila melanogaster with only a few exceptions. The base composition on these genomes is not balanced with the AT content (72.59%-85.15%) significantly higher than the GC content, and base usage bias exists with A (50.91% of AT content) and C (57.79% of GC content) base usage significantly higher than T and G. We identified 11 conservative regions based on the nucleotide and amino acid sequence conservation analysis of whole genome, and designed 26 pairs of universal primers for mitochondrial genome sequencing of Diptera with each pair of primers anchored to identify conservative regions. The target fragment amplified with each pair of primers is less than 1 200 bp in length. This set of primers was applied for sequencing Delia antiqua mitochondrial genome, and the results prove that the set of primers is efficient and operable.

Key words: Diptera, Delia antiqua, mitochondrial genome, gene structure, conservative regions, universal primers