Comparative mitogenomics of the zoonotic parasite Echinostoma revolutum resolves taxonomic relationships within the ' E. revolutum' species group and the Echinostomata (Platyhelminthes: Digenea)

Abstract

The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.

Keywords: Echinostoma revolutum; Echinostomatidae; Echinostomatoidea; mitochondrial genome; phylogenetic analysis; repeats; skewness value; ‘37-collar-spined’.

Fig. 1.

A schematic drawing of a circular map of the mitochondrial genome of Echinostoma revolutum (GenBank: MN496162). Protein-coding and ribosomal large and small subunit genes are abbreviated according to our previous publications (Le et al., 2016, 2019). The transfer RNA genes (tRNA) are marked with three letter-amino acid abbreviations (see: Table 2). The non-coding region (NCR) located between tRNA^Glu and cox3 consists of seven long (LRU1–7), four short repeat units (SRU1–4), and internal spacer sequence (IntS) between LRU7 and SRU4.

Fig. 2.

A maximum likelihood phylogenetic tree showing the position of Echinostoma revolutum (diamond symbol) based on the analysis of concatenated amino acid sequence data for the 12 mitochondrial proteins of 45 digenean species/strains. Thirteen families [Echinostomatidae, Fasciolidae, Himasthlidae, Echinochasmidae, Cyclocoelidae, Paramphistomidae, Gastrothylacidae, Notocotylidae, Troglotrematidae/(Paragonimidae), Heterophyidae, Opisthorchiidae, Diclocoeliidae, and Schistosomatidae] belonging to six superfamilies indicated by arrows, Echinostomatoidea (ECH), Paramphistomoidea (PAR), Pronocephaloidea (PRO), Troglotrematoidea (TRO), Opisthorchioidea (OPI), and Gorgoderoidea (GOR), are represented. Schistosoma haematobium (Platyhelminthes: Schistosomatidae) is included as an outgroup. Nodal support values evaluated using 1000 bootstrap resamplings are shown on each branch. The scale bar represents the number of substitutions per site. Accession numbers are given for each species/strains and country name (in bracket) of their origin (where available) at the end of each sequence.