Mitochondrial genome of Hypoderaeum conoideum - comparison with selected trematodes

Development of a duplex loop-mediated isothermal amplification together with lateral flow dipstick assay for the detection and discrimination of parasitic infections in chickens between cestodes belonging to genus Raillietina and trematodes in family Echinostomatidae

Most poultry farming that has been conducted by smallholders in Thailand are free-range and housing systems, which have risks of parasitic infection from the environment, particularly from tapeworms in the genus Raillietina and trematodes in the family Echinostomatidae. These have become important health problems in the poultry industry, causing low feed conversion ratios and leading to the loss of economic value. Our objective was to develop and validate a molecular technique based on duplex loop-mediated isothermal amplification (LAMP) together with lateral flow dipstick (LFD) assay for discriminating the infections between the genus Raillietina (R. echinobothrida, R. tetragona, and R. cesticillus) and the family Echinostomatidae (E. miyagawai, E. mekongi, E. macrorchis, and H. conoideum) in a single reaction. The developed assay was highly specific without cross-amplification with other poultry helminths and their hosts, at the optimized condition of 66 °C for 80 min. In addition, the results could be clearly visualized with the naked eye via LFD after incubating with probes at 66 °C for 10 min. The detection limit or analytical sensitivity of the Raillietina and Echinostomatidae groups were found to be 5 × 10-4 and 5 × 10-2 ng/μL, respectively. In clinical tests, the developed assay successfully detected parasites in naturally infected faeces from chickens in Thailand; results from McNemar's tests revealed no significant difference when compared to standard microscopy methods. Therefore, our assay is a viable alternative technique for an accurate and convenient diagnosis; it can also be used as a tool to guide anthelmintic drugs decision-making for treatments and farm management.

Mitogenomics of the zoonotic parasite Echinostoma miyagawai and insights into the evolution of tandem repeat regions within the mitochondrial non-coding control region

Echinostoma miyagawai is a cosmopolitan parasite within the Echinostomatidae and is a cause of human echinostomiasis. Species within the family have been a challenge to disentangle with E. miyagawai being synonyms of several other Echinostoma species. However, complete mitochondrial genomes have been shown to be vital in distinguishing echinostomatid species, but detailed comparisons of not only gene content but also structural features have been limited. Using long range sequencing techniques, the complete mitochondrial genome of E. miyagawai was sequenced and compared to other members of Echinostomatidae. In total 12 protein coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes were identified, as was an extensive noncoding control region (CR), consisting of 2 types of multiple tandem repeat units. Phylogenetic analyses of complete mitochondrial genomes corresponded to previous studies on single mitochondrial genes and nuclear ribosomal nuclear markers confirmed E. miyagawai to be within in the ‘Echinostoma revolutum’ group. The tandem repeat units found in the CR contained promoter sequences containing domains typical of initiation sites for replication and transcription as well as several palindromic regions which were shared between echinostomatid species. The study illustrates not only the utility complete mitogenomes in disentangling the relationship between these parasite species, but also provides some insight into the potential adaptations and other evolutionary processes that may govern the divergence of mitochondrial genomes for the first time in echinostomatids.

Risk of invasion and disease transmission by the Australasian freshwater snail Orientogalba viridis (Lymnaeidae): a field and experimental study

BACKGROUND

Biological invasions pose risks to the normal functioning of ecosystems by altering the structure and composition of several communities. Molluscs stand out as an extensively studied group given their long history of introduction by either natural or anthropogenic dispersal events. An alien population of the lymnaeid species Orientogalba viridis was first sighted in 2009 in southern Spain. In its native range (Australasian), this species is one of the main intermediate hosts of Fasciola hepatica, a major worldwide trematode parasite largely affecting humans, domestic animals and wildlife.

METHODS

We collected field populations of O. viridis from its native (Malaysia) and invaded (Spain) ranges. We performed detailed morphoanatomical drawings of the species and screened for natural infection of parasites. Individuals were molecularly characterized using ITS2 for comparison with existing sequences in a fine phylogeography study. We founded experimental populations at two different conditions (tropical, 26 °C and temperate, 21 °C) to study the life-history traits of exposed and non-exposed individuals to different F. hepatica isolates.

RESULTS

We found a 9% natural prevalence of trematode infection (98% similarity with a sequence of Hypoderaeum conoideum [Echinostomatidae]) in the Spanish field population. The haplotypes of O. viridis found in our study from Spain clustered with Australian haplotypes. Experimental infection with F. hepatica was successful in both experimental conditions but higher in tropical (87% prevalence) than in temperate (73%). Overall lifespan, however, was higher in temperate conditions (mean 32.5 ± 7.4 weeks versus 23.3 ± 6.5) and survivorship remained above 70% during the first 20 weeks. In parasite-exposed populations, life expectancy dropped from an overall 37.75 weeks to 11.35 weeks but still doubled the time for initial cercariae shedding. Cercariae shedding started at day 23 post-exposure and peaked between days 53 and 67 with an average of 106 metacercariae per snail.

CONCLUSIONS

Whether O. viridis will succeed in Europe is unknown, but the odds are for a scenario in which a major snail host of F. hepatica occupy all available habitats of potential transmission foci, ravelling the epidemiology of fasciolosis. This research provides a comprehensive understanding of O. viridis biology, interactions with parasites and potential implications for disease transmission dynamics, offering valuable insights for further research and surveillance.

First molecular insights into gastrointestinal helminths of domestic birds in the Caspian Sea Littoral of Iran with an emphasis on the One Health concern

The current investigation was carried out during the period from July 2022 to March 2023, aiming to investigate the prevalence of gastrointestinal helminths in domestic birds collected from traditional markets in Guilan province. One hundred forty-eight domestic birds, including chickens (Gallus gallus domesticus), domestic ducks (Anas platyrhynchos domesticus), greylag geese (Anser anser), and domestic turkeys (Meleagris gallopavo domesticus) were examined. Totally, 42.56% of the investigated birds were positive for helminthic parasites. Morphological analysis revealed varying infection rates among birds: Echinostoma revolutum (5.40%), Hypoderaeum conoideum (2.02%), Cloacotaenia megalops (0.67%), Hymenolepididae family (4.05%), Ascaridia galli (16.89%), and Heterakis gallinarum (4.72%). The investigation involved molecular analysis of the 18S and ITS1 + 5.8S + ITS2 rRNA gene regions. The findings indicated that the 18S region of nematode isolates exhibited a similarity of 92 to 100% with sequences in the GenBank, whereas trematode and cestode isolates showed a gene similarity ranging from 88 to 99%. The ITS regions of nematode, trematode, and cestode isolates exhibited genetic similarities ranging from 87 to 100%, 73-99%, and 75-99%, respectively. Furthermore, phylogenetic analysis confirmed the categorization of the identified species within the Ascaridiidae, Heterakidae, Hymenolepididae, and Echinostomatidae families, indicating their close affinity with previously documented species. Implementing precise control measures such as consistent monitoring, adequate sanitation protocols, and administering anthelmintic treatments is crucial for effectively managing parasitic infections in free-range and backyard poultry farms. Additionally, conducting further surveys is advisable to assess the impact of these parasites on the health and productivity of poultry in the investigated area.

A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences

New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.

Trematode Cercariae from Lymnaea gedrosiana in the Caspian Sea Littoral in Iran: a one health concern

INTRODUCTION

Lymnaea gedrosiana snails are hosts to a variety of trematode cercaria of public and veterinary health importance. In Guilan Province, Iran, a region with a high level of fish and bird farming and wetlands important for migratory birds, little is known about the trematode cercaria from L. gedrosiana.

METHODS

From April 2020 to October 2021, six freshwater sites in Guilan Province were sampled for Lymnaeidae snails three times per season (spring, summer, autumn and winter). Snails were exposed to light and heat to induce cercaria shedding and shredded cercaria were identified morphologically and molecularly.

RESULTS

In total, 5,712 Lymnaeidae snails were collected of which 3,288 (57.6%) were identified to be L. gedrosiana with 54.3% containing trematode cercaria. Snail and cercaria recovery were highest in the spring and summer. Trematode cercaria identified included Telorchis assula, Hypoderaeum conoideum, Apharyngostrigea pipientis, Sanguinicola cf. inermis, Opisthioglyphe ranae, Diplostomum pseudospathaceum, and Australapatemon burti.

DISCUSSION

The four trematodes D. pseudospathaceum, S. inermis, A. burti, and A. pipientis have not been previously reported in Iran; all four of these can infect migratory birds. The most common cercaria found, H. conoideum (18.3% of the snails) is of zoonotic importance. The third most common cercaria found, S. inermis (10.0% of the snails) is detrimental to fish production. Given the importance of the wetlands in the region for wildlife and migratory birds as well as the number of fish and bird farms in the area, efforts to control L. gedrosiana snails are needed to protect wildlife and human health. In addition, monitoring programs should be implemented to identify and prevent introductions of new trematode species.

Characterization of the complete mitochondrial genome of Plagiorchis multiglandularis (Digenea, Plagiorchiidae): Comparison with the members of Xiphidiatan species and phylogenetic implications

Plagiorchis multiglandularis Semenov, 1927 is a common fluke of birds and mammals, with significant impacts on animals and also human health. However, the systematics of Plagiorchiidae remain ambiguous. In the present study, the complete mitochondrial (mt) genome of P. multiglandularis cercariae was sequenced and compared with other digeneans in the order Xiphidiata. The complete circular mt genome of P. multiglandularis was 14,228 bp in length. The mitogenome contains 12 protein-coding genes and 22 transfer RNA genes. The 3' end of nad4L overlaps the 5' end of nad4 by 40 bp, while the atp8 gene is absent. Twenty-one transfer RNA genes transcribe products with conventional cloverleaf structures, while one transfer RNA gene has unpaired D-arms. Comparative analysis with related digenean trematodes revealed that A + T content of mt genome of P. multiglandularis was significantly higher among all the xiphidiatan trematodes. Phylogenetic analyses demonstrated that Plagiorchiidae formed a monophyletic branch, in which Plagiorchiidae are more closely related to Paragonimidae than Prosthogonimidae. Our data enhanced the Plagiorchis mt genome database and provides molecular resources for further studies of Plagiorchiidae taxonomy, population genetics and systematics.

The complete mitogenome of the Asian lung fluke Paragonimus skrjabini miyazakii and its implications for the family Paragonimidae (Trematoda: Platyhelminthes)

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T > G > C > A. Five Asian and American Paragonimus species and P. westermani had TTT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotremus. The P. westermani clade was clearly separate from remaining congeners. The latter clade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae.

The complete mitochondrial genome of Prosthogonimus cuneatus and Prosthogonimus pellucidus (Trematoda: Prosthogonimidae), their features and phylogenetic relationships in the superfamily Microphalloidea

Prosthogonimus cuneatus and Prosthogonimus pellucidus (Trematoda: Prosthogonimidae) are common flukes of poultry and other birds which can cause severe impacts on animal health and losses to the poultry industry. However, there are limited studies on the molecular epidemiology, population genetics, and systematics of Prosthogonimus species. In the present study, the complete mitochondrial (mt) genomes of P. cuneatus and P. pellucidus were determined to be 14,829 bp and 15,013 bp in length, respectively. Both mt genomes contain 12 protein-coding genes (PCGs) (cox1-3, nad1-6, nad4L, cytb, and atp6), 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. Our comparative analysis shows that the atp6 genes of P. cuneatus and P. pellucidus are longer than any previously published atp6 genes of other trematodes. The lengths of the atp6 genes of P. cuneatus and P. pellucidus in this study seem unusual, and should therefore be studied further. The mt genes of P. cuneatus and P. pellucidus are transcribed in the same direction, and the gene arrangements are identical to those of Plagiorchis maculosus, Tamerlania zarudnyi, and Tanaisia sp., but different from those of Eurytrema pancreaticum, Dicrocoelium chinensis, and Brachycladium goliath. The mt genome A + T contents of P. cuneatus and P. pellucidus are 64.47% and 65.34%, respectively. In the 12 PCGs, ATG is the most common initiation codon, whereas TAG is the most common termination codon. The sequence identity of the same 12 PCGs among the eight trematodes (P. cuneatus, P. pellucidus, Pl. maculosus, D. chinensis, E. pancreaticum, B. goliath, T. zarudnyi, Tanaisia sp.) of Xiphidiata are 55.5%-81.7% at the nucleotide level and 43.9%-82.5% at the amino acid level. The nucleotide similarities among the complete mt genomes of the eight trematodes range from 54.1%-81.5%. Phylogenetic analysis based on the aligned concatenated amino acid sequences of the 12 PCGs shows that P. cuneatus and P. pellucidus cluster together and are sister to T. zarudnyi and Tanaisia sp., and this clade is more closely related to E. pancreaticum, Dicrocoelium spp. and Lyperosomum longicauda in the family Dicrocoeliidae, than it is to species in the families Plagiorchiidae and Brachycladiidae. These are the first reported complete mt genomes of Prosthogonimidae, and these data will provide additional molecular resources for further studies of Prosthogonimidae taxonomy, population genetics, and systematics.

Characterization of complete mitochondrial genome and ribosomal operon for Carassotrema koreanum Park, 1938 (Digenea: Haploporidae) by means of next-generation sequencing data

We obtained new data on the complete mitochondrial DNA (mtDNA) and the ribosomal operon of the trematode Carassotrema koreanum (Digenea: Haploporata: Haploporidae), an intestinal parasite of Carassius auratus, using next-generation sequencing. The mtDNA of C. koreanum contained 13,965 bp, including 12 protein-coding genes, two ribosomal genes, 22 transport RNA (tRNA) genes and a non-coding region. The ribosomal operon of C. koreanum was 10,644 bp in length, including ETS1 (1449 bp), 18S ribosomal RNA (rRNA) gene (1988 bp), ITS1 ribosomal DNA (rDNA) (558 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (274 bp), 28S rRNA gene (4152 bp) and ETS2 (2066 bp). Phylogenetic analysis based on mtDNA protein-coding regions showed that C. koreanum was closely related to Parasaccocoelium mugili, a species from the same suborder Haploporata. Bayesian phylogenetic tree topology was the most reliable and confirmed the validity of the Haploporata. The results of sequence cluster analysis based on codon usage bias demonstrated some agreement with the results of the phylogenetic analysis. In particular, Schistosoma spp. were differentiated from the other members of Digenea and the members of Pronocephalata were localized within the same cluster. Carassotrema koreanum and P. mugili fell within different clusters. The grouping of C. koreanum and P. mugili within the same cluster was obtained on the basis of frequencies of 13 specified codons, of which three codon pairs were degenerate. A similarity was found between two haploporid species and two Dicrocoelium spp. in the presence of TTG start codon of the mitochondrial nad5 gene. Our results confirmed the taxonomical status of the Haploporata identified in the previous studies and revealed some characteristic features of the codon usage in its representatives.

Mitophylogenomics of the zoonotic fluke Echinostoma malayanum confirms it as a member of the genus Artyfechinostomum Lane, 1915 and illustrates the complexity of Echinostomatidae systematics

The complete mitochondrial genome (mitogenome or mtDNA) of the trematode Echinostoma malayanum Leiper, 1911 was fully determined and annotated. The circular mtDNA molecule comprised 12 protein-coding genes (PCGs) (cox1 - 3, cob, nad1 - 6, nad4L, atp6), two mitoribosomal RNAs (MRGs) (16S or rrnL and 12S or rrnS), and 22 transfer RNAs (tRNAs or trn), and a non-coding region (NCR) rich in long and short tandem repeats (5.5 LRUs/336 bp/each and 7.5 SRUs/207 bp/each). The atp8 gene is absent and the 3' end of nad4L overlaps the 5' end of nad4 by 40 bp. Special DHU-arm missing tRNAs for Serine were found for both tRNA^Ser1(AGN) and tRNA^Ser2(UCN). Codons of TTT (for phenylalanine), TTG (for leucine), and GTT (for valine) were the most, and CGC (for Arginine) was the least frequently used. A similar usage pattern was seen in base composition, AT and GC skewness for PCGs, MRGs, and mtDNA* (coding cox3 to nad5) in E. malayanum and Echinostomatidae. The nucleotide use is characterized by (T > G > A > C) for PCGs/mtDNA*, and by (T > G ≈ A > C) for MRGs. E. malayanum exhibited the lowest genetic distance (0.53%) to Artyfechinostomum sufrartyfex, relatively high to the Echinostoma congeners (13.20-13.99%), higher to Hypoderaeum conoideum (16.18%), and the highest to interfamilial Echinochasmidae (26.62%); Cyclocoelidae (30.24%); and Himasthlidae (25.36%). Topology indicated the monophyletic position between E. malayanum/A. sufrartyfex and the group of Echinostoma caproni, Echinostoma paraensei, Echinostoma miyagawai, and Echinostoma revolutum, rendering Hypoderaeum conoideum and unidentified Echinostoma species paraphyletic. The strictly closed genomic/taxonomic/phylogenetic features (including base composition, skewness, codon usage/bias, genetic distance, and topo-position) reinforced Echinostoma malayanum to retake its generic validity within the Artyfechinostomum genus.

First next-generation sequencing data for Haploporidae (Digenea: Haploporata): characterization of complete mitochondrial genome and ribosomal operon for Parasaccocoelium mugili Zhukov, 1971

The first data on a whole mitochondrial genome of Haploporidae, Parasaccocoelium mugili (Digenea: Haploporata: Haploporidae) was generated using the next-generation sequencing (NGS) approach. We sequenced the complete mitochondrial DNA (mtDNA) and ribosomal operon of Parasaccocoelium mugili, intestine parasite of mullet fish. The mtDNA of P. mugili contained 14,021 bp, including 12 protein-coding genes, two ribosomal genes, 22 tRNA genes, and non-coding region. The ribosomal operon of P. mugili was 8308 bp in length, including 18S rRNA gene (1981 bp), ITS1 rDNA (955 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (268 bp), 28S rRNA gene (4180 bp), and ETS (767 bp). We used the mtDNA protein-coding regions to make phylogenetic reconstructions of Haploporidae. Additionally, we performed the sequence cluster analysis based on codon usage bias of most of currently available mitochondrial genome data for trematodes. The observed gene arrangement in mtDNA sequence of P. mugili is identical to those of Plagiorchis maculosus (Rudolphi, 1802). Results of maximum likelihood (ML) phylogenetic analysis showed that P. mugili was closely related to Paragonimus species from the suborder Xiphidiata. The results of sequence cluster analysis based on codon usage bias showed that P. mugili has the highest similarity with Plagiorchis maculosus (Xiphidiata). Our results do not contradict to proposing a new suborder for Haploporoidea-Haploporata. On the basis of obtained results, the relationship between mitochondrial protein-coding gene rearrangements and synonymous nucleotide substitutions in mitochondrial genomes has been suggested.

Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (-0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

Characterization and phylogenetic properties of the complete mitochondrial genome of Fascioloides jacksoni (syn. Fasciola jacksoni) support the suggested intergeneric change from Fasciola to Fascioloides (Platyhelminthes: Trematoda: Plagiorchiida)

Fascioloides jacksoni (syn. Fasciola jacksoni, Cobbold, 1869) (Platyhelminthes: Echinostomatoidea), is a liver fluke that causes severe morbidity and mortality of Asian elephants (Elephas maximus maximus). Understandings on molecular diagnosis, epidemiology, genetics and evolution of this flatworm are limited. In this study, we present the complete mitochondrial DNA (mt) sequence of 14,952 bp obtained from an individual fluke and comparative characterization of mitogenomic features with fasciolids, primarily, Fascioloides magna and other taxa in the superfamily Echinostomatoidea. Taxonomic relationship within and between Echinostomatoidea, Opisthorchioidea and Paramphistomoidea in the order Plagiorchiida, are also taxonomically considered. The complete circular mt molecule of Fas. jacksoni contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes, and a non-coding region (NCR) rich in tandem repeat units. As common in digenean trematodes, Fas. jacksoni has the usual gene order, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes. The NCR located between tRNA^Glu (trnE) and cox3 contained nine nearly identical tandem repeat units (TRs of 113 bp each). Special DHU-arm missing tRNAs for Serine were found for both, tRNA^S1(AGN) and tRNA^S2(UCN). Base composition indicated that cox1 of Fas. jacksoni showed the lowest (11.8% to Fas. magna, 12.9 - 13.6% to Fasciola spp. and 18.1% to Fasciolopsis buski) and nad6 the highest divergence rate (19.2%, 23.8-26.5% and 27.2% to each fasciolid group), respectively. A clear bias in nucleotide composition, as of 61.68%, 62.88% and 61.54%, with a negative AT-skew of the corresponding values (-0.523, -0.225 and - 0.426) for PCGs, MRGs and mtDNA for Fas. jacksoni and likewise data for the fasciolids. Phylogenetic analysis confirmed the sister branch of Fas. jacksoni and Fas. magna with the nodal support of 100%, clearly separated from the taxonomically recognized Fasciola spp. With the previous studies, mitogenomic data presented in this study are strongly supportive for Fasciola jacksoni reappraisal as Fascioloides jacksoni in the Fascioloides genus.

Molecular phylogenetics and mitogenomics of three avian dicrocoeliids (Digenea: Dicrocoeliidae) and comparison with mammalian dicrocoeliids

Background

The Dicrocoeliidae are digenetic trematodes mostly parasitic in the bile ducts and gall bladder of various avian and mammalian hosts. Until recently their systematics was based on morphological data only. Due to the high morphological uniformity across multiple dicrocoeliid taxa and insufficient knowledge of relative systematic value of traditionally used morphological characters, their taxonomy has always been unstable. Therefore, DNA sequence data provide a critical independent source of characters for phylogenetic inference and improvement of the system.

Methods

We examined the phylogenetic affinities of three avian dicrocoeliids representing the genera Brachylecithum, Brachydistomum and Lyperosomum, using partial sequences of the nuclear large ribosomal subunit (28S) RNA gene. We also sequenced the complete or nearly complete mitogenomes of these three isolates and conducted a comparative mitogenomic analysis with the previously available mitogenomes from three mammalian dicrocoeliids (from 2 different genera) and examined the phylogenetic position of the family Dicrocoeliidae within the order Plagiorchiida based on concatenated nucleotide sequences of all mitochondrial genes (except trnG and trnE).

Results

Combined nucleotide diversity, Kimura-2-parameter distance, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently demonstrated that cox1, cytb, nad1 and two rRNAs were the most conserved and atp6, nad5, nad3 and nad2 were the most variable genes across dicrocoeliid mitogenomes. Phylogenetic analyses based on mtDNA sequences did not support the close relatedness of the Paragonimidae and Dicrocoeliidae and suggested non-monophyly of the Gorgoderoidea as currently recognized.

Conclusions

Our results show that fast-evolving mitochondrial genes atp6, nad5 and nad3 would be better markers than slow-evolving genes cox1 and nad1 for species discrimination and population level studies in the Dicrocoeliidae. Furthermore, the Dicrocoeliidae being outside of the clade containing other xiphidiatan trematodes suggests a need for the re-evaluation of the taxonomic content of the Xiphidiata.

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 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.

The complete mitochondrial genome of Echinostoma miyagawai: Comparisons with closely related species and phylogenetic implications

Echinostoma miyagawai (Trematoda: Echinostomatidae) is a common parasite of poultry that also infects humans. Es. miyagawai belongs to the "37 collar-spined" or "revolutum" group, which is very difficult to identify and classify based only on morphological characters. Molecular techniques can resolve this problem. The present study, for the first time, determined, and presented the complete Es. miyagawai mitochondrial genome. A comparative analysis of closely related species, and a reconstruction of Echinostomatidae phylogeny among the trematodes, is also presented. The Es. miyagawai mitochondrial genome is 14,416 bp in size, and contains 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding region (NCR). All Es. miyagawai genes are transcribed in the same direction, and gene arrangement in Es. miyagawai is identical to six other Echinostomatidae and Echinochasmidae species. The complete Es. miyagawai mitochondrial genome A + T content is 65.3%, and full-length, pair-wise nucleotide sequence identity between the six species within the two families range from 64.2-84.6%. The Es. miyagawai sequences is most similar to Echinostoma caproni. Sequence difference are 15.0-33.5% at the nucleotide level, and 8.6-44.2% at the amino acid level, among the six species, for the 12 protein-coding genes. ATG and TAG are the most common initiation and termination codons, respectively. Twenty of the Es. miyagawai transfer RNA genes transcribe products of the conventional cloverleaf structure, while two of the transfer RNA genes, namely trnS1^(AGC) and trnS2^(UGA), have unpaired D-arms. Phylogenetic analyses using our mitochondrial data indicate that Es. miyagawai is closely related to other Echinostomatidae species, except for Echinostoma hortense, which forms a distinct paraphyletic branch, and Echinochasmus japonicus, which is outside the clade containing all other Echinostomatidae species. These phylogenetic results support the elevation of subfamily Echinostomatidae. Our dataset also provides a significant resource of molecular markers to study the taxonomy, population genetics, and systematics of the echinostomatids.

Characterization of the mitochondrial genome sequences of the liver fluke Amphimerus sp. (Trematoda: Opisthorchiidae) from Ecuador and phylogenetic implications

Amphimerus Barker, 1911 is a liver fluke infecting several animal species and humans. Being a digenetic trematode of the Opisthorchiidae family, Amphimerus is closely related to the genera Metorchis, Clonorchis and Opisthorchis. Recently, a high prevalence of Amphimerus infection in humans, cats, and dogs had been demonstrated in a tropical Pacific region of Ecuador. Hence, we determined and characterized the entire mt genome sequences of adult liver flukes, morphologically identified as Amphimerus, collected in the endemic region of Ecuador, and examined its phylogenetic relationships with flukes in the Opisthorchiidae family using Bayesian inference (BI) based on the concatenated amino acid sequences and partial cox1 sequences. The complete mt genome sequence (15, 151 bp in length) of the Amphimerus sp. contains 35 genes, including 12 protein-coding genes (PCGs, without atp8), two rRNAs (rrnL and rrnS) and 21 tRNAs, lacking trnG. The gene content and arrangement of the Ecuadorian Amphimerus mt genome was similar to those of other trematodes in the Opisthorchiidae family. All genes in the circular mt genome of Amphimerus sp. are transcribed from the same strand in one direction, with the A + T content of 60.77%. Genetic distances between Amphimerus sp. and other genera in Opisthorchiidae were rather high, ranging from 26.86% to 28.75% at nucleotide level and 29.37%-31.12% at amino acid level. Phylogenetic analysis placed the Ecuadorian Amphimerus within the branch of Opisthorchiidae, but very distinct from Opisthorchis. Our results indicate that the liver fluke Amphimerus from Ecuador does not belong to the genus Opisthorchis, and that it should be assigned under the genus Amphimerus. The determination of the mt genome of the Ecuadorian Amphimerus provides a new genetic resource for future studies on taxonomy and molecular epidemiology of Opisthorchiidae trematodes.

The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5' end of nad4 overlapped with the 3' end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu . These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

Characterization of the complete mitochondrial genome of Uvitellina sp., representative of the family Cyclocoelidae and phylogenetic implications

Mitochondrial (mt) DNA has been useful in revealing the phylogenetic relationship of eukaryotic organisms including flatworms. Therefore, the use of mitogenomic data for the comparative and phylogenetic purposes is needed for those families of digenetic trematodes for which the mitogenomic data are still missing. Molecular data with sufficiently rich informative characters that can better resolve species identification, discrimination, and membership in different genera is also required for members of some morphologically difficult families of trematodes bearing few autapomorphic characters among its members. Here, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and the complete mt genome of the trematode Uvitellina sp. (Cyclocoelidae: Haematotrephinae) was determined and annotated. The mt genome of this avian trematode is 14,217 bp in length, containing 36 genes plus a single non-coding region. The ITS rDNA sequences were used for the pairwise sequence comparison of Uvitellina sp. with European cyclocoelid species, and the mitochondrial 12 protein-coding genes (PCGs) and two ribosomal RNA genes were used to evaluate the position of the family within selected trematodes. The ITS rDNA analysis of Uvitellina sp. showed less nucleotide differences with Hyptiasmus oculeus (16.77%) than with other European cyclocoelids (18.63-23.58%). The Bayesian inference (BI) analysis using the 12 mt PCGs and two rRNA genes supported the placement of the family Cyclocoelidae within the superfamily Echinostomatoidea (Plagiorchiida: Echinostmata). The availability of the mt genome sequences of Uvitellina sp. provides a novel resource of molecular markers for phylogenetic studies of Cyclocoelidae and other trematodes.

Prevalence, Morphological and Molecular Phylogenetic Analyses of the Rabbit Pinworm, Passalurus ambiguus Rudolphi 1819, in the Domestic Rabbits Oryctolagus cuniculus

INTRODUCTION

Passalurus ambiguus, a pinworm nematode parasite, infects domestic and wild rabbits, hares, and rodents worldwide.

MATERIALS AND METHODS

The current parasitological study was performed during January-December 2016, to investigate helminth parasites infecting the domestic rabbit species Oryctolagus cuniculus at the Department of Animal Production, Faculty of Agriculture, Cairo University, Cairo, Egypt.

RESULTS

Of the twenty rabbit specimens examined for gastrointestinal nematodes, 75% were infected with adult oxyurid species, which were morphologically characterized using light and scanning electron microscopy studies. The oxyurid species had a triangular mouth opening surrounded by simple lips with four cephalic papillae and a pair of lateral amphidial pores with three teeth-like structures, an esophagus divided into a cylindrical corpus and globular bulb supported internally with tri-radiate valvular apparatus, and four caudal papillae distributed on the posterior end of males with a single short protruding spicule and ovijector apparatus opening ventrally by the vulva, surrounded by protruded lips in female worms. The species were compared morphometrically with other Passalurus species described previously; light differences were found in different body part sizes. Molecular characterization based on 18 small subunit (SSU) rDNA sequences showed ~ 85% similarity with other Chromadorea species. A preliminary genetic comparison between the 18S rDNA sequences of the isolated parasite and those of other oxyurid species suggested that it belonged to Passalurus ambiguus. The 18S rDNA sequence of the parasite was deposited in GenBank (accession no., MG310151.1).

CONCLUSION

The 18S rDNA gene of P. ambiguus was shown to yield a unique genetic sequence that confirms its taxonomic position within the Oxyuridae family.

Morphological and molecular characterisation of three Indian Neascus-type metacercariae (Digenea: Diplostomidae)

Diplostomid digeneans are important parasites whose larval stages infect freshwater snails and fish as first and second intermediate hosts respectively. Diplostomid digeneans as adults are parasitic in many fish-eating birds and mammals. Our understanding of the species diversity of diplostomid digeneans remains incomplete, especially in the Indian sub-continent. Here, we describe three Neascus-type metacercariae (N. hanumanthai, N. gussevi, and N. xenentodoni) from freshwater fish specimens of Channa punctata (Bloch 1793), Trichogaster fasciata (Bloch and Schneider 1801) and Xenentodon cancila (Hamilton, 1822) respectively, collected in India. Next, we characterised these metacecariae using nuclear (28S and ITS1) and mitochondrial DNA (cox1) to determine their systematic and phylogenetic position. Molecular identification using interspecific variation for all three molecular markers revealed a closer relationship between N. hanumanthai and N. gussevi (1.9%-2.4%) than either of N. hanumanthai and N. gussevi to N. xenentodoni (3.1%-3.7% and 4.4%-4.0% respectively). In phylogenetic analyses, estimated by neighbour-joining (NJ) and maximum likelihood (ML) methods, N. gussevi and N. hanumanthai nested as sister groups of Posthodiplostomum Dubois, 1936 for all three markers used; N. xenentodoni, however, nested as a sister taxa of all other diplostomes when using 28S and ITS1 and nested as a sister taxa of Bolbophorus, Alaria and Neodiplostomum using cox1. These findings suggest that N. hanumanthai and N. gussevi are members of Posthodiplostomum, but that N. xenentodoni belongs to a separate and unknown genus. Similarly, by proteomics, we found that the cox1 protein sequences and structures were similar between N. hanumanthai and N. gussevi but distinct for N. xenentodoni.

Threading: A novel insilico indagation method for genetic characterization of some diplostomoid metacercariae (Digenea:Diplostomidae Poirier, 1886)

The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools. Various aspects have been utilized herein for re-validation and infallible discrimination of Trematode diplostomoid metacercariae (Tetracotyle lucknowensis Pandey, 1971; T. xenentodoni Chakrabarti, 1970; T. fausti Rai and Pande, 1969; T. muscularius Chakrabarti, 1970 and Diplostomulum minutum Pandey, 1968), the infective stage in the life cycle, causing severe damage to fish host, whose adults are found mainly in fish eating birds and mammals.

Complete mitochondrial genome of the giant liver fluke Fascioloides magna (Digenea: Fasciolidae) and its comparison with selected trematodes

Background

Representatives of the trematode family Fasciolidae are responsible for major socio-economic losses worldwide. Fascioloides magna is an important pathogenic liver fluke of wild and domestic ungulates. To date, only a limited number of studies concerning the molecular biology of F. magna exist. Therefore, the objective of the present study was to determine the complete mitochondrial (mt) genome sequence of F. magna, and assess the phylogenetic relationships of this fluke with other trematodes based on the mtDNA dataset.

Findings

The complete F. magna mt genome sequence is 14,047 bp. The gene content and arrangement of the F. magna mt genome is similar to those of Fasciola spp., except that trnE is located between trnG and the only non-coding region in F. magna mt genome. Phylogenetic relationships of F. magna with selected trematodes using Bayesian inference (BI) was reconstructed based on the concatenated amino acid sequences for 12 protein-coding genes, which confirmed that the genus Fascioloides is closely related to the genus Fasciola; the intergeneric differences of amino acid composition between the genera Fascioloides and Fasciola ranged 17.97–18.24 %.

Conclusions

The determination of F. magna mt genome sequence provides a valuable resource for further investigations of the phylogeny of the family Fasciolidae and other trematodes, and represents a useful platform for designing appropriate molecular markers.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1699-7) contains supplementary material, which is available to authorized users.

The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years

The evolution of technologies to explore parasite biology at a detailed level has made significant advances in recent years, particularly with the development of omic-based strategies. Whilst extensive efforts have been made in the past to develop therapeutic and prophylactic control strategies for trematode parasites, only the therapeutic anthelmintic approach can be regarded as usable in clinical practice. Currently, there is no commercialised prophylactic strategy (such as vaccination) for protection of the definitive host against any trematode parasite. Since 2010 in particular, the integration of omic technologies, including liquid chromatography-mass spectrometry (LC-MS) and next-generation sequencing (NGS), has been increasingly reported in trematode-related studies. Both LC-MS and NGS facilitate a better understanding of the biology of trematodes and provide a promising route to identifying clinically important biological characteristics of parasitic trematodes. In this review, we focus on the application, advantages, and disadvantages of omic technologies (LC-MS and NGS) in trematode research within the past 5 years and explore the use and translation of the omic-based research results into practical tools to deal with infection.

Characterization of the complete mitochondrial genome sequence of Homalogaster paloniae (Gastrodiscidae, Trematoda) and comparative analyses with selected digeneans

Gastrodiscidae species are neglected but significant paramphistomes in small ruminants, which can lead to considerable economic losses to the breeding industry of livestock. However, knowledge about molecular ecology, population genetics, and phylogenetic analysis is still limited. In the present study, we firstly sequenced and analyzed the full mitochondrial (mt) genome of Homalogaster paloniae (14,490 bp). The gene contents and organization of the H. paloniae mt genome is the same as that of other digeneans, such as Fasciola hepatica and Paramphistomum cervi. It is interesting that unlike other paramphistomes, H. paloniae is flat in shape which is similar with Fasciola, such as F. hepatica. Phylogenetic analysis of H. paloniae and other 17 selected digeneans using concatenated amino acid sequences of the 12 protein-coding genes showed that Gastrodiscidae is closely related to Paramphistomidae and Gastrothylacidae. The availability of the mt genome sequence of H. paloniae should provide an important foundation for further molecular study of Gastrodiscidae and other digeneans.

The complete mitochondrial genome of Orthocoelium streptocoelium (Digenea: Paramphistomidae) for comparison with other digeneans

Orthocoelium streptocoelium is a common paramphistome species parasitizing the rumen and/or reticulum of small ruminants, leading to significant losses. This study first determined the complete mitochondrial (mt) genome of O. streptocoelium. The complete mt genome of O. streptocoelium was amplified, sequenced, assembled, analysed and then compared with those of other digeneans. The entire mt genome of O. streptocoelium is 13,800 bp in length, which is smaller than those of other digeneans except for Opisthorchis viverrini. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the O. streptocoelium mt genome is the same as those of other digeneans except for Schistosoma haematobium and Schistosoma spindale. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes representing 16 digeneans were conducted to assess the relationship of O. streptocoelium with other digeneans. The result indicated that O. streptocoelium is closely related to Paramphistomum cervi and Fischoederius elongates, which is in accordance with their relationships by taxonomy. This complete mt genome of O. streptocoelium enriched the mitochondrial genome data of paramphistomes and provided important molecular markers for diagnostics and studies of population variation, epidemiology, ecology and evolution of O. streptocoelium and other digeneans.

Mitochondrial genome of Ogmocotyle sikae and implications for phylogenetic studies of the Notocotylidae trematodes

Ogmocotyle spp. (Trematoda: Digenea: Notocotylidae) are neglected but important trematodes that can infect numerous mammal species, causing significant economic losses to livestock industries. However, there have been few studies on the molecular ecology of these trematodes. We amplified and sequenced the complete mitochondrial (mt) genome of Ogmocotyle sikae (14,307 bp). The gene content and gene arrangement of O. sikae mt genome was similar to that of Dicrocoelium chinensis, except that trnE and trnG were reversed. Phylogenetic analysis of O. sikae and selected parasites using Bayesian inference was performed based on concatenated amino acid sequence datasets conceptually translated from the 12 protein-coding genes. The results indicated that the family Notocotylidae is related to the family Paramphistomatidae. Our description of O. sikae mt genome provides a significant resource of molecular markers for future comparative studies of the Notocotylidae and other trematodes.

The complete mitochondrial genome of rabbit pinworm Passalurus ambiguus: genome characterization and phylogenetic analysis

Passalurus ambiguus (Nematda: Oxyuridae) is a common pinworm which parasitizes in the caecum and colon of rabbits. Despite its significance as a pathogen, the epidemiology, genetics, systematics, and biology of this pinworm remain poorly understood. In the present study, we sequenced the complete mitochondrial (mt) genome of P. ambiguus. The circular mt genome is 14,023 bp in size and encodes of 36 genes, including 12 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The mt gene order of P. ambiguus is the same as that of Wellcomia siamensis, but distinct from that of Enterobius vermicularis. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference (BI) showed that P. ambiguus was more closely related to W. siamensis than to E. vermicularis. This mt genome provides novel genetic markers for studying the molecular epidemiology, population genetics, systematics of pinworm of animals and humans, and should have implications for the diagnosis, prevention, and control of passaluriasis in rabbits and other animals.