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Background  The family Hoplopleuridae contains at least 183 species of blood-sucking lice, which widely parasitize both mice and rats. Fragmented mitochondrial (mt) genomes have been reported in two rat lice ( Hoplopleura kitti  and  H. akanezumi ) from this family, but some minichromosomes were unidentified in their mt genomes.    Methods  We sequenced the mt genome of the rat louse  Hoplopleura  sp. with an Illumina platform and compared its mt genome organization with  H. kitti  and  H. akanezumi .    Results  Fragmented mt genome of the rat louse  Hoplopleura  sp. contains 37 genes which are on 12 circular mt minichromosomes. Each mt minichromosome is 1.8–2.7 kb long and contains 1–5 genes and one large non-coding region. The gene content and arrangement of mt minichromosomes of  Hoplopleura  sp. ( n  = 3) and  H. kitti  ( n  = 3) are different from those in  H. akanezumi  ( n  = 3). Phylogenetic analyses based on the deduced amino acid sequences of the eight protein-coding genes showed that the  Hoplopleura  sp. was more closely related to  H. akanezumi  than to  H. kitti , and then they formed a monophyletic group.    Conclusions  Comparison among the three rat lice revealed variation in the composition of mt minichromosomes within the genus  Hoplopleura .  Hoplopleura  sp. is the first species from the family Hoplopleuridae for which a complete fragmented mt genome has been sequenced. The new data provide useful genetic markers for studying the population genetics, molecular systematics and phylogenetics of blood-sucking lice.

Variation of mitochondrial minichromosome composition in Hoplopleura lice (Phthiraptera: Hoplopleuridae) from rats