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Background  Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus  Taenia  includes a diversity of tapeworm parasites of significant human and veterinary importance. Here we add complete sequences of the mt genomes of  T. multiceps ,  T. hydatigena  and  T. pisiformis , to a data set of 4 published mtDNAs in the same genus. Seven complete mt genomes of  Taenia  species are used to compare and contrast variation within and between genomes in the genus, to estimate a phylogeny for the genus, and to develop novel molecular markers as part of an extended mitochondrial toolkit.    Results  The complete circular mtDNAs of  T. multiceps ,  T. hydatigena  and  T. pisiformis  were 13,693, 13,492 and 13,387 bp in size respectively, comprising the usual complement of flatworm genes. Start and stop codons of protein coding genes included those found commonly amongst other platyhelminth mt genomes, but the much rarer initiation codon GTT was inferred for the gene  atp 6 in  T. pisiformis . Phylogenetic analysis of mtDNAs offered novel estimates of the interrelationships of  Taenia . Sliding window analyses showed  nad 6,  nad 5,  atp 6,  nad 3 and  nad 2 are amongst the most variable of genes per unit length, with the highest peaks in nucleotide diversity found in  nad 5. New primer pairs capable of amplifying fragments of variable DNA in  nad 1,  rrn S and  nad 5 genes were designed  in silico  and tested as possible alternatives to existing mitochondrial markers for  Taenia .    Conclusions  With the availability of complete mtDNAs of 7  Taenia  species, we have shown that analysis of amino acids provides a robust estimate of phylogeny for the genus that differs markedly from morphological estimates or those using partial genes; with implications for understanding the evolutionary radiation of important  Taenia . Full alignment of the nucleotides of  Taenia  mtDNAs and sliding window analysis suggests numerous alternative gene regions are likely to capture greater nucleotide variation than those currently pursued as molecular markers. New PCR primers developed from a comparative mitogenomic analysis of  Taenia  species, extend the use of mitochondrial markers for molecular ecology, population genetics and diagnostics.

bmc genomics

Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance