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

Le, Thanh Hoa; Pham, Linh Thi Khanh; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Saijuntha, Weerachai; Rajapakse, R. P. V. J.; Lawton, Scott P

doi:10.1017/s0031182020000128

Cited by 15 publications

(30 citation statements)

References 44 publications

(140 reference statements)

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“…6). This difference between phylogenies based on mitochondrial nucleotides and amino acids sequences is consistent with our previous study [26] and several other studies, including those published very recently [50].…”

Section: Phylogeny Of Xiphidiatan Trematodes and Other Selected Tremasupporting

confidence: 93%

Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications

et al. 2021

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Background The Eucotylidae Cohn, 1904 (Superfamily: Microphalloidea), is a family of digeneans parasitic in kidneys of birds as adults. The group is characterized by the high level of morphological similarities among genera and unclear systematic value of morphological characters traditionally used for their differentiation. In the present study, we sequenced the complete or nearly complete mitogenomes (mt genome) of two eucotylids representing the genera Tamerlania (T. zarudnyi) and Tanaisia (Tanaisia sp.). They represent the first sequenced mt genomes of any member of the superfamily Microphalloidea. Methods A comparative mitogenomic analysis of the two newly sequenced eucotylids was conducted for the investigation of mitochondrial gene arrangement, contents and genetic distance. Phylogenetic position of the family Eucotylidae within the order Plagiorchiida was examined using nucleotide sequences of mitochondrial protein-coding genes (PCGs) plus RNAs using maximum likelihood (ML) and Bayesian inference (BI) methods. BI phylogeny based on concatenated amino acids sequences of PCGs was also conducted to determine possible effects of silent mutations. Results The complete mt genome of T. zarudnyi was 16,188 bp and the nearly complete mt genome of Tanaisia sp. was 13,953 bp in length. A long string of additional amino acids (about 123 aa) at the 5′ end of the cox1 gene in both studied eucotylid mt genomes has resulted in the cox1 gene of eucotylids being longer than in all previously sequenced digeneans. The rrnL gene was also longer than previously reported in any digenean mitogenome sequenced so far. The TΨC and DHU loops of the tRNAs varied greatly between the two eucotylids while the anticodon loop was highly conserved. Phylogenetic analyses based on mtDNA nucleotide and amino acids sequences (as a separate set) positioned eucotylids as a sister group to all remaining members of the order Plagiorchiida. Both ML and BI phylogenies revealed the paraphyletic nature of the superfamily Gorgoderoidea and the suborder Xiphidiata. Conclusions The average sequence identity, combined nucleotide diversity and Kimura-2 parameter distances between the two eucotylid mitogenomes demonstrated that atp6, nad5, nad4L and nad6 genes are better markers than the traditionally used cox1 or nad1 for the species differentiation and population-level studies of eucotylids because of their higher variability. The position of the Dicrocoeliidae and Eucotylidae outside the clade uniting other xiphidiatan trematodes strengthened the argument for the need for re-evaluation of the taxonomic content of the Xiphidiata.

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Section: Phylogeny Of Xiphidiatan Trematodes and Other Selected Tremasupporting

confidence: 93%

Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications

et al. 2021

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“…Likewise ITS-2 of H. taichui also showed repetitive sequences. The presence ofrepeats in the internal transcribed spacers of trematodes has been reported for several taxa, including those in Fasciolidae, Heterophyidae, Opisthorchiidae, Paramphistomatidae, Schistosomatidae and others (Dzikowski et al, 2004;Zheng et al, Sato et al, 2010;Tatonova et al, 2012;Le et al, 2020). The presence of repeats, variation in length and sequence variation, within and between species, all contribute to difficulties when trying to align ITS regions and this particularly is not suitable for deep-level phylogenetic analysis of species (Blair, 2006).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analyses of ribosomal transcription units from Haplorchis taichui and H. pumilio species of Heterophyidae (Platyhelminthes: Opisthorchiata)

Ha¹,

Khue²,

Quyền³

et al. 2021

Vietnam J. Biotechnol.

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Heterophyidiasis caused by minute intestinal flukes becomes of public concern in many countries worldwide. Haplorchis taichui and H. pumilio, belonging to the family Heterophyidae (Platyhelminthes: Trematoda) are two of many infecting humans and commonly found in Vietnam. Sequence study of these two small intestinal flukes is still very limited, hence we need more prospective markers for taxonomic identification and classification. This study provides complete coding sequence of the ribosomal transcription units (rTU) from H. taichui and H. pumilio (Vietnamese samples) and demonstrates the use of complete 28S rDNA sequences for phylogenetic analysis.The complete coding sequence of the rTU (from 5' 18S to 3' 28S), consisting of complete 18S, ITS-1, 5.8S, ITS2 and complete 28S rRNA genes and spacers, from H. taichui (7,268 bp) and H. pumilio (7,416 bp) from human hosts in Vietnam, were determined and annotated. The 18S and 5.8S genes of both species were of the same length (1,992 bp/18S, 160 bp/5.8S), but 28S genes differed (3,875 bp/H. taichui and 3,870 bp/H. pumilio). ITS-1 in H. taichui (797 bp) and ITS-2 in H. pumilio (280 bp) do not contain tandem repeat units (TRUs), while ITS-1 in H. pumilio (1,106 bp) contains 3 TRUs of 136 bp/each and 2 TRUs of 116 bp/each and ITS-2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each). A phylogenetic tree inferred from the alignment of complete 28S rDNA sequences of 32 trematode strains/species, including 2 Vietnamese Haplorchis spp. and 24 species of 8 families in the suborders Xiphidiata (families Nanophyetidae, Paragonimidae, Collyriclidae), Opisthorchiata (Heterophyidae, Opisthorchiidae), and Echinostomata (Echinostomatidae, Fasciolidae). and Schistosoma japonicum of the family Schistosomatidae is used as an outgroup. The topology of the phylogenetic tree clearly confirmed the status of the Vietnamese H. taichui and H. pumilio species. These species gathered in a group (in the family Heterophyidae) clearly identified in the position of "sister” group to those in the family Opisthorchiidae (suborder Opisthorchiata, superfamily Opisthorchioidea).

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“…Thus, the nad 1 phylogenetic tree revealed 3 lineages of E. revolutum ; Asian, Eurasian, and American lineages [ 111 ]. The complete mitochondrial genome (17,030 bp) of E. revolutum was obtained and characterized by Le et al [ 112 ] in comparison with 9 echinostome species, including E. caproni , E. miyagawai , and E. paraensei . They concluded that E. revolutum grouped in a monophyletic subclade as a sister taxon to E. miyagawai and paraphyletic to other echinostomatids in the Echinostomatidae [ 112 ].…”

Section: Species Of 37-collar-spined Echinostoma Gmentioning

confidence: 99%

“…The complete mitochondrial genome (17,030 bp) of E. revolutum was obtained and characterized by Le et al [ 112 ] in comparison with 9 echinostome species, including E. caproni , E. miyagawai , and E. paraensei . They concluded that E. revolutum grouped in a monophyletic subclade as a sister taxon to E. miyagawai and paraphyletic to other echinostomatids in the Echinostomatidae [ 112 ]. A multiplex PCR technique targeting the nad 1 gene has been developed for differential detection of 4 medically important echinostome species, including E. revolutum [ 113 ].…”

Section: Species Of 37-collar-spined Echinostoma Gmentioning

confidence: 99%

“…This species has been listed among the 37-collar spined ‘ E. revolutum ’ spp. by Kostadinova and Gibson [ 26 ], Fried and Graczyk [ 8 ], Maldonado and Lanfredi [ 92 ], Toledo et al [ 9 ], Nagataki et al [ 72 ], and Le et al [ 112 ]. However, taxonomic attention on this species has been scarce, and there has been no information on molecular characteristics.…”

Section: Species Of 37-collar-spined Echinostoma Gmentioning

confidence: 99%

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Taxonomy of Echinostoma revolutum and 37-Collar-Spined Echinostoma spp.: A Historical Review

et al. 2020

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Echinostoma flukes armed with 37 collar spines on their head collar are called as 37-collar-spined Echinostoma spp. (group) or ‘Echinostoma revolutum group’. At least 56 nominal species have been described in this group. However, many of them were morphologically close to and difficult to distinguish from the other, thus synonymized with the others. However, some of the synonymies were disagreed by other researchers, and taxonomic debates have been continued. Fortunately, recent development of molecular techniques, in particular, sequencing of the mitochondrial (nad1 and cox1) and nuclear genes (ITS region; ITS1-5.8S-ITS2), has enabled us to obtain highly useful data on phylogenetic relationships of these 37-collar-spined Echinostoma spp. Thus, 16 different species are currently acknowledged to be valid worldwide, which include E. revolutum, E. bolschewense, E. caproni, E. cinetorchis, E. deserticum, E. lindoense, E. luisreyi, E. mekongi, E. miyagawai, E. nasincovae, E. novaezealandense, E. paraensei, E. paraulum, E. robustum, E. trivolvis, and Echinostoma sp. IG of Georgieva et al., 2013. The validity of the other 10 species is retained until further evaluation, including molecular analyses; E. acuticauda, E. barbosai, E. chloephagae, E. echinatum, E. jurini, E. nudicaudatum, E. parvocirrus, E. pinnicaudatum, E. ralli, and E. rodriguesi. In this review, the history of discovery and taxonomic debates on these 26 valid or validity-retained species are briefly reviewed.

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

Cited by 15 publications

References 44 publications

Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications

Mitochondrial genomes of two eucotylids as the first representatives from the superfamily Microphalloidea (Trematoda) and phylogenetic implications

Phylogenetic analyses of ribosomal transcription units from Haplorchis taichui and H. pumilio species of Heterophyidae (Platyhelminthes: Opisthorchiata)

Taxonomy of Echinostoma revolutum and 37-Collar-Spined Echinostoma spp.: A Historical Review

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