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

MORPHOLOGICAL OBSERVATION AND DETAILED MOLECULAR CHARACTERIZATION OF FISCHOEDERIUS ELONGATUS (DIGENEA: GASTROTHYLACIDAE) FROM THE RUMEN OF DOMESTIC CATTLE IN CAMBODIA

Fischoederius elongatus (Poirier, 1883) is a common rumen fluke found in Asia and Africa. Nucleotide sequence data for F. elongatus have been reported but are limited to certain ribosomal and mitochondrial DNA regions. High diversity in the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) haplotypes has been reported in some Asian countries. Some researchers have advocated the possibility of cryptic species within F. elongatus based on the high genetic diversity within the species as well as the genetic distance within and between sister species. However, the number of examined parasites, hosts, and geographic regions was limited in these studies, and the intraspecific variation of the species remains unclear. Therefore, additional studies are required to provide more insight into the genetic variation of F. elongatus. This study characterized F. elongatus in the rumen of Cambodian cattle and documented its genetic information and intraspecific variation. The flukes were morphologically identified, and the molecular structure of the 28S and COI regions was analyzed. The partial sequences of 28S from the 45 specimens yielded 2 genotypes, and the 28S sequences of F. elongatus seem to be highly conserved in Cambodia. In contrast, partial sequences of COI from 44 specimens exhibited 29 distinct haplotypes, and the similarity among the haplotypes was 92.9-99.7%, indicating high diversity of the COI sequence in the Cambodian F. elongatus population. In both 28S and COI phylogenetic trees, the present sequences formed a single clade with Gastrothylacidae species; however, the 4 genera within the family did not form genus-specific clades. These results suggest that complete species identification of Gastrothylacidae is difficult to perform based solely on the 28S and COI sequences. The molecular population genetics of F. elongatus in Cambodia were found to be highly diverse in COI sequences, and a star-like haplogroup was also detected. In addition, some haplotypes were identical to those from neighboring countries, such as India and Thailand, and no distinct country-specific haplogroups were found. Therefore, ancient domestication, artificial migration, and the contemporary import of host cattle may have involved genetic populations in these countries. Highly diverse COI haplotypes were found with few or no differences in morphology, and the diverse haplotypes found in the current and previous studies were unlikely to originate from cryptic species.

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications

Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT- and GC-skews were - 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein-coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in "trnE-trnG" and "trnG-trnE". Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

The complete mitochondrial genome of 3 species of allocreadiids (Digenea, Allocreadiidae): characterization and phylogenetic position within the order Plagiorchiida

Trematodes of the family Allocreadiidae are primarily found in the intestines of freshwater fishes around the world. The family includes 15 genera and c. 130 species. The last 2 decades have witnessed an increase in the genetic library of its species. Molecular data have been crucial for species delimitation and species description within Allocreadiidae and for understanding their evolutionary and biogeographical history and classification. Here, the mitogenomes of 3 species of allocreadiids were obtained using high throughput sequencing methods. Mitogenomes were compared with other members of the order Plagiorchiida to determine their molecular composition, gene rearrangement and phylogenetic interrelationships. The complete circular mitogenomes of Allocreadium lobatum, Creptotrematina aguirrepequenoi and Wallinia mexicana were 14 424, 13 769 and 13 924 bp long respectively, comprising 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. Gene arrangements were identical to other Xiphidiatan trematodes. Phylogenetic analyses using the mitogenomes revealed Allocreadiidae as a monophyletic group closely related to other members of the suborder Xiphidiata; A. lobatum was yielded as the sister taxon of C. aguirrepequenoi + W. mexicana. Our study increases the complete mitochondrial genome library of trematodes and strengthens our understanding of the phylogenetic relationships and classification of this parasite group.

Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts

Parasites have evolved a variety of astonishing strategies to survive within their hosts, yet the most challenging event in their personal chronicles is the passage from one host to another. It becomes even more complex when a parasite needs to pass through the external environment. Therefore, the free-living stages of parasites present a wide range of adaptations for transmission. Parasitic flatworms from the group Digenea (flukes) have free-living larvae, cercariae, which are remarkably diverse in structure and behavior.1,2 One of the cercariae transmission strategies is to attain a prey-like appearance for the host.3 This can be done through the formation of a swimming aggregate of several cercariae adjoined together by their tails.4 Through the use of live observations and light, electron, and confocal microscopy, we described such a supposedly prey-mimetic colony comprising cercariae of two distinct morphotypes. They are functionally specialized: larger morphotype (sailors) enable motility, and smaller morphotype (passengers) presumably facilitate infection. The analysis of local read alignments between the two samples reveals that both cercaria types have identical 18S, 28S, and 5.8S rRNA genes. Further phylogenetic analysis of these ribosomal sequences indicates that our specimen belongs to the digenean family Acanthocolpidae, likely genus Pleorchis. This discovery provides a unique example and a novel insight into how morphologically and functionally heterogeneous individuals of the same species cooperate to build colonial organisms for the purpose of infection. This strategy bears resemblance to the cooperating castes of the same species found among insects.5.

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.

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

Trematodes of the genus Ogmocotyle are intestinal flukes that can infect a variety of definitive hosts, resulting in significant economic losses worldwide. However, there are few studies on molecular data of these trematodes. In this study, the mitochondrial (mt) genome of Ogmocotyle ailuri isolated from red panda (Ailurus fulgens) was determined and compared with those from Pronocephalata to investigate the mt genome content, genetic distance, gene rearrangements and phylogeny. The complete mt genome of O. ailuri is a typical closed circular molecule of 14 642 base pairs, comprising 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. All genes are transcribed in the same direction. In addition, 23 intergenic spacers and 2 locations with gene overlaps were determined. Sequence identities and sliding window analysis indicated that cox1 is the most conserved gene among 12 PCGs in O. ailuri mt genome. The sequenced mt genomes of the 48 Plagiorchiida trematodes showed 5 types of gene arrangement based on all mt genome genes, with the gene arrangement of O. ailuri being type I. Phylogenetic analysis using concatenated amino acid sequences of 12 PCGs revealed that O. ailuri was closer to Ogmocotyle sikae than to Notocotylus intestinalis. These data enhance the Ogmocotyle mt genome database and provide molecular resources for further studies of Pronocephalata taxonomy, population genetics and systematics.

Rich but morphologically problematic: an integrative approach to taxonomic resolution of the genus Neospirorchis (Trematoda: Schistosomatoidea)

Neospirorchis Price, 1934 is a genus of blood flukes that infect the cardiovascular system, including vessels surrounding the nervous systems of marine turtles. Although the genus comprises just two named species, the available molecular data suggest substantial richness which has not yet been formally described. The lack of description of species of Neospirorchis is probably explained by their small, slender, elongate bodies, which allow them to infect numerous organs and vessels in their hosts, such as the heart and peripheral vessels of nervous system, endocrine organs, thymus, mesenteric vessels, and gastrointestinal submucosa. This morphology and site of infection means that collecting good quality, intact specimens is generally difficult, ultimately hampering the formal description of species. Here we supplement limited morphological samples with multi-locus genetic data to formally describe four new species of Neospirorchis infecting marine turtles from Queensland, Australia and Florida, USA; Neospirorchis goodmanorum n. sp. and Neospirorchis deburonae n. sp. are described from Chelonia mydas, Neospirorchis stacyi n. sp. is described from Caretta caretta, and Neospirorchis chapmanae n. sp. from Ch. mydas and Ca. caretta. The four new species are delineated from each other and the two known species based on the arrangement of the male and female reproductive organs, on the basis of cytochrome c oxidase subunit 1 (cox1), internal transcribed spacer 2 (ITS2), and 28S ribosomal DNA (rDNA) molecular data, site of infection, and host species. Molecular evidence for three further putative, presently undescribable, species is also reported. We propose that this integrated characterisation of species of Neospirorchis, based on careful consideration of host, molecular and key morphological data, offers a valuable solution to the slow rate of descriptions for this important genus. We provide the first known life cycle data for Neospirorchis in Australian waters, from Moreton Bay, Queensland; consistent with reports from the Atlantic, sporocysts were collected from a terebellid polychaete and genetically matched to an unnamed species of Neospirorchis infecting Ch. mydas from Queensland and Florida.

Biomphalaria straminea as an Intermediate Host of a Renal Trematode Species of the Genus Tanaisia (Trematoda: Eucotylidae) in Brazil

PURPOSE

Eucotylid trematodes are parasites of the urinary system of birds with a cosmopolitan distribution. Despite the importance of these flukes, fundamental aspects of their biology, such as intermediate hosts and larval morphology, are poorly known. Herein, the potential involvement of aquatic mollusks in the transmission of a species of Tanaisia is reported for the first time.

METHODS

During the search of non-emergent larval stages of trematodes in mollusks collected from an urban waterbody from Brazil in February of 2021, 1 out of 18 specimens (5.5%) of Biomphalaria straminea was found harboring sporocysts, cercariae and encysted metacercariae morphologically compatible with those described for eucotylid species. Sequences generated for 28S, ITS-2, and cox1 molecular markers were compared with sequences available in GenBank and subjected to phylogenetic analyses.

RESULTS

Molecular analyses revealed parasite affiliation with members of the genus Tanaisia, given it groped in a strongly supported clade with species of this genus included in the 28S phylogenetic tree. The larvae tentatively identified as Tanaisia sp. can be conspecific with an unpublished isolate of Tanaisia valida found in birds in South Brazil (100% similarity in 28S and ITS-2).

CONCLUSION

Biomphalaria straminea is reported as a natural host of a species of Tanaisia for the first time. This finding highlights the possibility, so far unknown, of transmission of species of the family Eucotylidae in aquatic environments.

The first modern morphological description of Cercaria pennata and molecular evidence of its synonymy with Pronoprymna ventricosa in the Black Sea

During the parasitological examination of molluscs Abra segmentum obtained from the Black Sea basin, parthenitae belonging to the family Faustulidae were found. The cercariae were obtained by natural emergence and were studied using differential interference contrast microscopy and scanning electron microscopy. Specimens resemble Cercaria pennata ex Tapes rugatus which was described from the Sevastopol area, in the shape and length of the body, tail length, location and shape of internal organs, suckers, pharynx, testicular rudiments, and the number and position of longitudinal lamellae on the tail finlets. To date, there are only limited descriptions of the parthenitae of C. pennata without detailed measurements, thus the taxonomic position of the individuals studied needs thorough revision and molecular verification. According to the molecular analyses, C. pennata was identical to that of published sequences of Pronoprymna ventricosa.

Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae) are two important parasites in wood frogs, which have large infection rates and essential importance of ecology, economy and society. In this study, the complete mitochondrial (mt) genomes of D. japonicus and D. mehari were sequenced, then compared with other related trematodes in the superfamily Paramphistomoidea. The complete circular mt sequence of D. japonicus and D. mehari were 14,210 bp and 14,179 bp in length, respectively. Both mt genomes comprised 36 functional subunits, consisting of 12 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one non-coding region. The mt genes of D. japonicus and D. mehari were transcribed in the same direction, and the gene arrangements were identical to those of Paramphistomoidea trematodes. In the 12 PCGs, GTG was the most common initiation codon, whereas TAG was the most common termination codon. All tRNAs had a typical cloverleaf structure except tRNA Ser1. A comparison with related Paramphistomoidea trematode mt genomes suggested that the cox1 gene of D. mehari was the longest in these trematodes. Phylogenetic analyses revealed that Paramphistomoidea trematodes formed a monophyletic branch, Paramphistomidae and Gastrothylacidae were more closely related than Diplodiscidae. And the further analysis with Pronocephalata branch found that the flukes parasitic in amphibians (frogs) formed one group, and the flukes from ruminants (cattle, sheep, ect) formed another group. Our study demonstrated the importance of sequencing mt genomes of D. japonicus and D. mehari, which will provide significant molecular resources for further studies of Paramphistomoidea taxonomy, population genetics and systematics.

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The complete mt genomes of Diplodiscus japonicus and D. mehari were determined first time.

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There is only one NCR in Diplodiscus japonicus and D. mehari complete mt genomes.

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Phylogenetic analyses revealed two monophyletic groups for the flukes parasitic in amphibians and ruminants.

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.

New trematode species Lecithostaphylus halongi n. sp. (Zoogonidae, Microphalloidea) and Gymnotergestia strongyluri n. sp. (Fellodistomidae, Gymnophalloidea) from beloniform fishes in Vietnam

In this study we described two new trematode species, Lecithostaphylus halongi n. sp. (Zoogonidae, Lecithostaphylinae) and Gymnotergestia strongyluri n. sp. (Fellodistomidae, Tergestiinae), on the basis of morphological and molecular data. Adult worms of these two species were collected from, respectively, Hemiramphus spp. (Hemiramphidae) and Strongylura strongylura (Belonidae) caught in the coastal waters of Vietnam. Adult worms of L. halongi n. sp. are morphologically close to Lecithostaphylus gibsoni Cribb, Bray & Barker, 1992 ex Abudefduf whitleyi from Heron Island and Lecithostaphylus depauperati Yamaguti, 1970 ex Hemiramphus depauperatus from Hawaii, but differ from these species in having a larger cirrus sac and a different arrangement of vitelline fields. They also differ from Lecithostaphylus brayi Cabañas-Granillo, Solórzano-García, Mendoza-Garfias & Pérez-Ponce de León, 2020 in the 28S ribosomal DNA (rDNA) sequence data at the interspecific level. Adult worms of G. strongyluri n. sp. ex S. strongylura are morphologically similar to Gymnotergestia chaetodipteri, the only previously known species of this genus, described from Chaetodipterus faber in Jamaica. The new species differs from G. chaetodipteri in body shape, testicular arrangement and the size of the pharynx and eggs. The 28S rDNA-based phylogenetic analysis indicates that G. strongyluri n. sp. is closely related to Tergestia spp., rendering Tergestia paraphyletic. Genetic divergence values between G. strongyluri n. sp. and Tergestia spp. are similar to those among species in the genera Tergestia, Steringophorus and Proctoeces. Our molecular results indicate that G. strongyluri n. sp. and Tergestia spp. may belong the same genus, but additional molecular data are needed for the final conclusion.