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Background   Dictyocaulus  species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or “husk”). There has been ongoing controversy surrounding the validity of some  Dictyocaulus  species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt) genomes of  Dictyocaulus viviparus  (from  Bos taurus ) with  Dictyocaulus  sp. cf.  eckerti  from red deer ( Cervus elaphus ), used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies.    Methods  The mt genomes were amplified from single adult males of  D. viviparus  and  Dictyocaulus  sp. cf.  eckerti  (from red deer) by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), also employing data for other strongylids for comparative purposes.    Results  The circular mt genomes were 13,310 bp ( D. viviparus ) and 13,296 bp ( Dictyocaulus  sp. cf.  eckerti ) in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between  D. viviparus  and  Dictyocaulus  sp. cf.  eckerti , and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both  D. viviparus  and  Dictyocaulus  sp. cf.  eckerti  were closely related, and grouped to the exclusion of selected members of the superfamilies Metastrongyloidea, Trichostrongyloidea, Ancylostomatoidea and Strongyloidea.    Conclusions  Consistent with previous findings for nuclear ribosomal DNA sequence data, the present analyses indicate that  Dictyocaulus  sp. cf.  eckerti  (red deer) and  D. viviparus  are separate species. Barcodes in the two mt genomes and proteomes should serve as markers for future studies of the population genetics and/or epidemiology of these and related species of  Dictyocaulus .

Assessment of the genetic relationship between Dictyocaulus species from Bos taurus and Cervus elaphus using complete mitochondrial genomic datasets