Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae

Abstract

Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1–3, nad 1–6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.

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

“…The complete mitochondrial genome of E. revolutum (Fröhlich, 1802) Rudolphi, 1809, was 17,030 bp in size; the longest of all the Echinostomatoidea to date sequenced, although the mitogenome of E. paraensei (KT008005) was claimed longer, 20,298 bp, but some of 5,600 nucleotides were only of estimation (Liu et al ., 2014; Yang et al ., 2015; Le et al ., 2016; Ma et al ., 2016, 2017; Fu et al ., 2019; Suleman et al ., 2019; Li et al ., 2019 a , 2019 b ).…”

“…japonicus (Le et al ., 2016) and two cyclocoelids, Uvitellina sp. and T. cymbius (Suleman et al ., 2019; Li et al ., 2019 a ). It was considerably longer than many fasciolids, such as Fa.…”

“…The complete mitochondrial genome of E. revolutum (Fröhlich, 1802) Rudolphi, 1809, was 17,030 bp in size; the longest of all the Echinostomatoidea to date sequenced, although the mitogenome of E. paraensei (KT008005) was claimed longer, 20,298 bp, but some of 5,600 nucleotides were only of estimation (Liu et al, 2014;Yang et al, 2015;Le et al, 2016;Ma et al, 2016Ma et al, , 2017Fu et al, 2019;Suleman et al, 2019;Li et al, 2019aLi et al, , 2019b. The length of the mt genome of E. revolutum seemed to be one of the longest among trematodes fully obtained to date, shorter than the estimated, partially sequenced congener E. paraensei, but was slightly longer than other echinostomids, including H. conoideum (Yang et al, 2015), E. miyagawai (Fu et al, 2019;Li et al, 2019b), Ech.…”

“…in the Echinostomatoidea lack complete mitochondrial genomic data. Currently, only four of the nine species of the ‘ E. revolutum ’ group, including E. caproni , E. paraensei , E. miyagawai , E. hortense (Saijuntha et al ., 2011 c ), and a few species within the Echinostomata suborder have complete mitochondrial genomes available (Yang et al ., 2015; Fu et al ., 2019; Suleman et al ., 2019; Li et al ., 2019 a , 2019 b ).…”

“…magna, P. ohirai, repetitive units either of long or short sequences and even various quantity within a species, frequently occurred and commonly found (Le et al, 2001(Le et al, , 2016(Le et al, , 2019Liu et al, 2014;Ma et al, 2016Ma et al, , 2017Fu et al, 2019;Li et al, 2019b). Interestingly, none of the repetitive units was found in E. caproni, H. conoideum and T. cymbius (Yang et al, 2015;Li et al, 2019a). The occurrence of repetitive sequences in tandem order in many species certainly is one of the most interesting genomic features, specifying the high-level polymorphism in the NCRs of digenean trematodes.…”