The fragmented mitochondrial genomes of two Linognathus lice reveal active minichromosomal recombination and recombination hotspots.

Evidence for recombination between mitochondrial (mt) minichromosomes has been reported in sucking lice, but it is still not clear how frequent mt minichromosomal recombination occurs. We sequenced the mt genomes of the cattle louse and the goat louse Both species have 10 mt minichromosomes, and seven of them have the same gene content and gene arrangement. Comparison of mt karyotypes revealed numerous inter-minichromosomal recombination events in the evolution of species. Minichromosome merger, gene duplication and gene translocation occurred in the lineage leading to lice. After the divergence of and , duplication, degeneration, deletion and translocation of genes also occurred independently in each species. Most of the recombination events in the species occurred upstream of either or , indicating these two locations were hotspots for inter-minichromosomal recombination. Our results provide an important perspective on mt genome evolution in metazoans.