The complete mitochondrial genome of a parasitic flatworm Senga ophiocephalina (Cestoda: Bothriocephalidae).

Mitochondrial DNA of nematodes undergoes frequent rearrangements, so it is a very good model for studying the mitochondrial genome evolution. The complete mitochondrial genome of a parasitic nematode Senga ophiocephalina was sequenced and annotated. The 13,816 bp-long genome contained 12 protein-coding genes (atp8 gene was missing), two ribosomal RNAs, 22 transfer RNAs, and a 391 bp non-coding region. Phylogenetic analysis showed that S. ophiocephalina forms a monophyletic cluster with the remaining two Bothriocephalidae species.

Mitochondrial DNA of nematodes undergoes frequent rearrangements, which makes it a good model for studying the mechanisms of mitochondrial genome evolution (Hu & Gasser 2006). Phylogenetic relationships within Bothriocephalidea, a relatively recently established order (previously Pseudophyllidea) of tapeworms that mostly parasitise on teleost fish (Kuchta et al. 2008), are still disputable (Brabec et al. 2015). To fully resolve these, it will be necessary to employ a marker capable of providing good phylogenetic resolution. The complete mitogenome provides better phylogenetic resolution and precision relative to traditional markers (Sebastián et al. 2011), but mitogenome sequences are currently available only for two Schyzocotyle (syn. Bothriocephalus) species in Bothriocephalidae family (syn. Ptychobothriidae). Hence, to help future researches resolve the phylogenetic relationships within this order, we have sequenced the whole genome of an Asian parasitic fish tapeworm belonging to a different genus within the Bothriocephalidae, Senga ophiocephalina.

Senga ophiocephalina specimen was collected from the Zhegui reservoir (103°19′ E, 23°56′ N), near Mile city in Yunnan province. The specimen is stored in the Aquatic Organisms Museum of Guangdong Ocean University under the accession number SO02052015YN. DNA was extracted using the Aidlab kit. Twenty-two primer pairs were used to amplify the entire mitochondrial genome sequence (GenBank accession number: KX434430). The genome is rather small (13,816 bp), all genes are transcribed in the same direction, and it lacks the Atp8 gene, all of which are common features for nematode genomes (usually 13.6–14.3 kb). Hence, it contains only 12 protein-coding genes, along with the usual 22 tRNAs and 2 rRNAs. Eleven protein-coding genes use AUG start codon and UAG or UAA stop codons. Cox3 gene uses GUG as start and an abbreviated UAA (UU- -) as stop codon. All these are common in invertebrate mtDNA (Hu & Gasser 2006). Similar to a parasitic nematode Strongyloides stercoralis (Hu et al. 2003), the studied genome also has extremely high T content (55.9%) and extremely low C content (8.3%), resulting in a very strong A + T bias (70.1%).

Phylogenetic position of S. ophiocephalina was estimated using maximum-likelihood, implemented in RaxmlGUI (with 1000 bootstrap replications) (Silvestro & Michalak 2012), and the Bayesian inference (BI), implemented in MrBayes version 3.26 (default settings, four MCMC chains, 6.34 × 106 generations) (Ronquist & Huelsenbeck 2003), approaches. Mitogenome sequences of all 23 available cestode species, and a trematode Dicrocroelium dendriticum as outgroup, were retrieved from the GenBank. Analyses were performed on concatenated 12 mitochondrial protein-coding genes and 2 rRNA genes (12,444 bp). GTR + G + I was chosen as the best nucleotide substitution model for both analyses. Apart from a somewhat ambiguous position of Versteria mustelae, both dendrogram topologies were identical (Figure 1; only BI dendrogram is shown). Senga ophiocephalina formed a monophyletic cluster with the remaining two Bothriocephalidae species (with high statistical support), which then formed a sister clade with Diphylobothriidae family. Apart from the ambivalent position of Dipyliidae, the overall dendrogram topology is highly congruent with the results of Cheng et al. (2016).

Figure 1.

Phylogenetic dendrogram showing the evolutionary relationships among S. ophiocephalina (highlighted by a black dot), all 23 cestode species are available in GenBank and a trematode D. dendriticum as an outgroup. Maximum-likelihood and the Bayesian analyses were performed using partial genomes. Scale bar corresponds to the estimated number of substitutions per site. Both bootstrap support (first number) and the Bayesian posterior probability values (second number) are displayed next to the nodes. Values lower than 70 are displayed as –. GenBank accession numbers indicated in the figure.