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Background  Mitochondrial (mt) genome sequences are widely used to understand phylogenetic relationships among parasites. However, no complete mt genome sequence is available in the family Anoplocephalidae to date. This study sequenced and annotated the complete mt genome of  Anoplocephala perfoliata  (Anoplocephalidae), and investigated its phylogenetic relationships with other species from the families Hymenolepididae, Dipylidiidae and Taeniidae of the order Cyclophyllidea using the amino acid sequences of the 12 proteins in their mt genomes.    Methods  The complete mt genome of  A. perfoliata  was amplified by Long-range PCR, sequenced using primer walking and annotated by comparing with those of other cestodes. Its phylogenetic relationship with the species from the families Hymenolepididae, Dipylidiidae and Taeniidae was inferred using the 12 protein sequences based on Maximum likelihood and Bayesian methods.    Results  The complete circular mt genome sequence for  A. perfoliata  is 14,459 bp in size, and includes 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The mt gene arrangement of  A. perfoliata  is identical to those of previously reported  Hymenolepis diminuta  (Hymenolepididae) and  Dipylidium caninum  (Dipylidiidae), but slightly different from those of other taeniids due to an order switch between tRNA(S2) and tRNA(L1). The phylogenetic analyses showed that the Dipylidiidae was more closely related to Anoplocephalidae and Hymenolepididae than to Taeniidae. The relationship among the four families obtained by Maximum likelihood and Bayesian inferences based on predicted amino acid sequences of protein-coding genes is consistent with that based on their mt gene arrangement similarities.    Conclusions  This study determined the first mt genome for the family Anoplocephalidae, providing rich sources for selecting useful molecular markers for ecological and phylogenetic studies. Analyses on mt genome sequences of the four families of cestodes provide novel insights into their phylogenetic relationships. Of couse, more taxon sampling is necessary for future phylogenetic studies of these cestodes using mt genome sequences.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-1172-z) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of Anoplocephala perfoliata, the first representative for the family Anoplocephalidae