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Background  The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly  Libelloides macaronius  is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders.    Results  The mitochondrial genome of  L. macaronius  is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of  trnC . The  L. macaronius  genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for  cox1 , which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid  rrnS  and  rrnL  genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect  rrnL . The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs.    Conclusions  The new genome shares many features with known neuropteran genomes but differs in its low A+T content. Comparative analysis of neuropterid mitochondrial genes showed that they experienced distinct evolutionary patterns. Both tRNA families and ribosomal RNAs show composite substitution pathways. The neuropterid mitochondrial genome is characterized by a complex evolutionary history.

The mitochondrial genome of the ascalaphid owlfly Libelloides macaronius and comparative evolutionary mitochondriomics of neuropterid insects