Exploring the genetic diversity of Tylodelphys (Diesing, 1850) metacercariae in the cranial and body cavities of Mexican freshwater fishes using nuclear and mitochondrial DNA sequences, with the description of a new species

Tegumental topography and molecular characterisation of two trematodes (Platyhelminthes: Digenea) from Clarias gariepinus (Burchell, 1822) in Kenya

The discoveries of new taxonomic features of digenean species through the application of contemporary techniques, such as scanning electron microscopy (SEM) and molecular analysis are still growing. Two species of trematodes Glossidium pedatum and Tylodelphys mashonensis from the intestine and vitreous humour of Clarias gariepinus were recovered from Lake Ol'Bolossat, Kenya. The two endo-helminths were prepared for morphological examination using SEM and molecular characterisation. Additional morphological features were observed for G. pedatum such as domed papillae in the anterior extremity and a protruding cirrus which was unarmed, laterally folded and with a blunt tip as the first such observation for the genus and led to additional characteristics of the diagnosis of the genus. Tylodelphys mashonensis was characterised by a round oral sucker and tribocytic organ rounded with rows of papillae symmetrically arranged. The molecular analyses using ribosomal marker 28S large subunit (LSU) rDNA and mitochondrial (mtDNA) cytochrome c oxidase subunit 1 (cox1) for both G. pedatum and T. mashonensis confirmed the identity of the species and their phylogenetic relationship within the subclass Digenea. This study provides the first mitochondrial (mt)DNA sequence for G. pedatum and also extends the geographical record of two parasites to Kenya.

Description and Phylogenetic Relationships of Anhingatrema n. gen. (Digenea: Diplostomidae) with Two New Species from New World Anhingas (Aves: Anhingidae)

PURPOSE

The Diplostomidae is a globally distributed family of digeneans that parasitize a wide variety of tetrapod definitive hosts. Recent molecular phylogenetic studies have revealed unknown diplostomid diversity in avian hosts throughout the New World. Herein, we provide descriptions of a novel genus of diplostomids with two new species.

METHODS

Two species of diplostomids belonging to the new genus were collected from anhinga birds in Mississippi (USA) and Brazil. Partial nuclear 28S ribosomal and mitochondrial cox1 genes were sequenced. Ribosomal data were used for phylogenetic inference.

RESULTS

Both species of Anhingatrema n. gen. were positioned in a 100% supported, monophyletic clade in the phylogenetic tree. The molecular phylogenetic position and a combination of morphological features (e.g., presence of pseudosuckers, testes shape and orientation) supported erection of the new genus. Anhingatrema overstreeti n. sp. and Anhingatrema cararai n. sp. are morphologically similar, but differ in size of and ratios associated with pseudosuckers. The two species differ by 2% of 28S sequences and 13.8% of cox1 sequences. Comparison of DNA sequences revealed that Diplostomidae gen. sp. in GenBank (MZ314151) is conspecific with An. overstreeti n. sp.

CONCLUSION

Anhingatrema n. gen. is the sixth genus of diplostomids known from anhingas worldwide. Anhingatrema cararai n. sp. is the first diplostomid to be reported from anhingas in South America. Combined with previous studies, the molecular phylogenies revealed at least two host switches to anhingas from other birds during the evolutionary history of the Diplostomidae.

New record of Tylodelphys metacercariae (Diplostomidae) from Perccottus glenii (Odontobutidae) and their phylogenetic assessment

Metacercariae of Tylodelphys sp. were found in the abdominal cavity of the Chinese sleeper (Perccottus glenii) collected in Liaoning Province and Inner Mongolia Autonomous Region of China. The sequences of the mitochondrial cox1 gene and ribosomal ITS1-5.8S rDNA-ITS2 region were obtained and used for molecular identification and phylogenetic assessment of this parasite species. Results of phylogenetic analyses based on ITS and cox1 markers showed that the metacercariae of Tylodelphys sp. ex P. glenii from China were conspecific with specimens of Tylodelphys sp. collected by Sokolov et al. (2013) from the same fish-host species captured earlier in West Siberia, Russia. The examined Tylodelphys sp. ex. P. glenii is the only member of the genus whose metacercariae parasitise the abdominal cavity of fish in northern Eurasia. Tylodelphys sp. ex P. glenii clustered with T. darbyi, T. immer, T. podicipina, and Tylodelphys sp. of Soldánová et al., 2017 based on mitochondrial DNA markers, and with T. darbyi, T. immer, T. kuerepus, and T. schreuringi using nuclear DNA markers.

Molecular phylogeny supports invalidation of Didelphodiplostomum and Pharyngostomoides (Digenea: Diplostomidae) and reveals a Tylodelphys from mammals

Alaria, Didelphodiplostomum and Pharyngostomoides are among genera of diplostomid digeneans known to parasitize mammalian definitive hosts. Despite numerous recent molecular phylogenetic studies of diplostomids, limited DNA sequence data is available from diplostomids parasitic in mammals. Herein, we provide the first 28S rDNA and cox1 mtDNA sequences from morphologically identified, adult specimens of Didelphodiplostomum and Pharyngostomoides. Newly generated 28S sequences were used to infer the phylogenetic interrelationships of these two genera among other major lineages of diplostomoideans. The phylogeny based on 28S and a review of morphology clearly suggests that Pharyngostomoides should be considered a junior synonym of Alaria, while Didelphodiplostomum should be considered a junior synonym of Tylodelphys. Pharyngostomoides procyonis (type species), Pharyngostomoides adenocephala and Pharyngostomoides dasyuri were transferred into Alaria as Alaria procyonis comb. nov., Alaria adenocephala comb. nov. and Alaria dasyuri comb. nov.; Didelphodiplostomum variabile (type species) and Didelphodiplostomum nunezae were transferred into Tylodelphys as Tylodelphys variabilis comb. nov. and Tylodelphys nunezae comb. nov. In addition, Alaria ovalis comb. nov. (formerly included in Pharyngostomoides) was restored and transferred into Alaria based on a morphological study of well-fixed, adult specimens and the comparison of cox1 DNA sequences among Alaria spp. The diplostomid genus Parallelorchis was restored based on review of morphology.

Metacercariae in the brain of Erythrinus cf. erythrinus (Characiformes: Erythrinidae) from Iguazú National Park (Argentina): do they belong to Dolichorchis lacombeensis (Digenea, Diplostomidae)?

In Argentina, the family Diplostomidae is composed of eight genera: Austrodiplostomum Szidat & Nani; Diplostomum von Nordmann; Dolichorchis Dubois; Hysteromorpha Lutz; Neodiplostomum Railliet; Posthodiplostomum Dubois; Sphincterodiplostomum Dubois; and Tylodelphys Diesing. During a parasitological survey of fishes from the Iguazú National Park we detected diplostomid metacercariae in the brain of Erythrinus cf. erythrinus. Fish were caught using crab traps, transported alive to the field laboratory, cold-anaesthetized and euthanized by cervical dissection. Some metacercariae were heat-killed in water and fixed in 10% formalin and others were preserved in alcohol 96% for DNA extraction. They were sequenced for the partial segment of the 28S rDNA, internal transcribed spacer (ITS) rDNA and cytochrome c oxidase subunit I (COI) mtDNA genes. Phylogenetic reconstruction was carried out using Bayesian inference and the proportion (p) of absolute nucleotide sites (p-distance) was obtained. In the 28S rDNA tree, the metacercaria sequenced grouped as Dolichorchis sp. The COI mtDNA p-distance between the metacercariae with Dolichorchis lacombeensis was 0.01. There is a small number of ITS sequences for the Diplostomidae family deposited in the GenBank. The oral sucker, ventral sucker, holdfast organ and the distance between oral and ventral suckers are larger in the adult compared with the metacercariae. Additionally, hind-body length and width are larger in the adult due to the development of the genital complex. Further studies using an integrative approach will help confirm the affiliation of other species to the genus Dolichorchis.

The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes

Background

Genetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. However, challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers’ ability to provide sufficient species-level resolution limited their utility. This study presented novel and broadly applicable primers using the mitochondrial 12S and 16S rRNA genes for Digenea and aimed to show their suitability as alternative genetic markers for molecular identification of orders Plagiorchiida, Echinostomida, and Strigeida.

Results

Our results revealed that the mitochondrial 12S and 16S rRNA genes are suitable for trematode molecular identification, with sufficient resolution to discriminate closely related species and achieve accurate species identification through phylogenetic placements. Moreover, the robustness of our newly designed primers to amplify medically important parasitic trematodes encompassing three orders was demonstrated through successful amplification. The convenience and applicability of the newly designed primers and adequate genetic variation of the mitochondrial rRNA genes can be useful as complementary markers for trematode molecular-based studies.

Conclusions

We demonstrated that the mitochondrial rRNA genes could be alternative genetic markers robust for trematode molecular identification and potentially helpful for DNA barcoding where our primers can be widely applied across the major Digenea orders. Furthermore, the potential of the mitochondrial rRNA genes for molecular systematics can be explored, enhancing their appeal for trematode molecular-based studies. The novelty of utilizing the mitochondrial rRNA genes and the designed primers in this study can potentially open avenues for species identification, discovery, and systematics in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08302-4.

Assessing the genetic diversity of the metacercariae of Posthodiplostomum minimum (Trematoda: Diplostomidae) in Middle American freshwater fishes: one species or more?

Trematode taxonomy is mainly based on the morphological traits of adults. The identification of metacercariae is challenging because such traits are not developed in larval forms, and they even may show some level of morphological variability. Studies testing the potential correspondence between morphological differences and genetic variation of parasites are still lacking. The metacercariae of Posthodiplostomum minimum are probably the diplostomids more widely distributed in North and Middle American freshwater fish, and their intraspecific morphological variability has been attributed to the effect exerted by the host. Here, we tested the hypothesis whether they represent a single species, or a species complex by assessing the genetic divergence and phylogenetic relationships of metacercariae sampled from several host species in a wide geographical range across Middle America. The internal transcribed spacers (ITS1-5.8S-ITS2), and the mitochondrial COI gene were sequenced for 124 and 55 metacercariae, respectively. Phylogenetic analysis inferred from ITS sequences uncovered six well-supported monophyletic lineages. The six lineages show no correspondence to any Posthodiplostomum species for which sequences are available thus far in GenBank. Lineages exhibit some degree of host specificity; Lineages I, II, IV and V are primarily parasites of cyprinodontiforms of the families Poeciliidae, Goodeidae, Profundulidae and Fundulidae. In poeciliids there are at least four candidate species of Posthodiplostomum, some of them occurring in sympatry; instead, Lineages II and VI are exclusively parasites of cichlids. This study contributes to our understanding of the diversity of larval forms of diplostomids and provides an opportunity to further study their life cycles.

Molecular phylogeny of Diplostomum, Tylodelphys, Austrodiplostomum and Paralaria (Digenea: Diplostomidae) necessitates systematic changes and reveals a history of evolutionary host switching events

The Diplostomidae Poirier, 1886 is a large, globally distributed family of digeneans parasitic in intestines of their definitive hosts. Diplostomum and Tylodelphys spp. are broadly distributed, commonly reported, and the most often sequenced diplostomid genera. The majority of published DNA sequences from these genera originated from larval stages only, which typically cannot be identified to the species level based on morphology alone. We generated partial large ribosomal subunit (28S) rRNA and cytochrome c oxidase subunit 1 (cox1) mtDNA gene sequences from 14 species/species-level lineages of Diplostomum, six species/species-level lineages of Tylodelphys, two species/species-level lineages of Austrodiplostomum, one species previously assigned to Paralaria, two species/species-level lineages of Dolichorchis and one unknown diplostomid. Our DNA sequences of 11 species/species-level lineages of Diplostomum (all identified to species), four species/species-level lineages of Tylodelphys (all identified to species), Austrodiplostomum compactum, Paralaria alarioides and Dolichorchis lacombeensis originated from adult specimens. 28S sequences were used for phylogenetic inference to demonstrate the position of Paralaria alarioides and Dolichorchis spp. within the Diplostomoidea and study the interrelationships of Diplostomum, Tylodelphys and Austrodiplostomum. Our results demonstrate that two diplostomids from the North American river otter (P. alarioides and a likely undescribed taxon) belong within Diplostomum. Further, our results demonstrate the non-monophyly of Tylodelphys due to the position of Austrodiplostomum spp., based on our phylogenetic analyses and morphology. Furthermore, the results of phylogenetic analysis of 28S confirmed the status of Dolichorchis as a separate genus. The phylogenies suggest multiple definitive host-switching events (birds to otters and among major avian groups) and a New World origin of Diplostomum and Tylodelphys spp. Our DNA sequences from adult digeneans revealed identities of 10 previously published lineages of Diplostomum and Tylodelphys, which were previously identified to genus only. The novel DNA data from this work provide opportunities for future comparisons of larval diplostomines collected in ecological studies.

Morphological and molecular characterization of Austrodiplostomum compactum metacercariae in the eyes and brains of fishes from the Ivaí River, Brazil

Austrodiplostomum spp. (Platyhelminthes: Digenea) are endoparasites with a broad geographic distribution in South America. During the larval stage, they parasitize the eyes, brains, muscles, gill, kidneys and swim bladder of a wide variety of fishes. The metacercariae of Austrodiplostomum spp. have several morphological characteristics during development, but are very similar among species, which makes it necessary to use molecular tools to contribute to the elucidation during the larval stage. The objective of this study was to perform morphological and molecular analyses of Austrodiplostomum sp. found in specimens of Hypostomus sourced from the Ivaí River in the state of Paraná, Brazil. Of the 93 analyzed specimens (H. hermanni [n = 50], H. albopunctatus [n = 9], Hypostomus sp. 1 [n = 24], and Hypostomus sp. 2 [n = 10]), 60 were parasitized. A total of 577 Austrodiplostomum sp. metacercariae was collected from the infected hosts; DNA from seven of these samples was extracted, amplified, and sequenced. The morphological data associated with the genetic distance values and the relationships observed in the COI gene tree, indicate that all metacercariae were A. compactum. This is the first record of A. compactum parasitizing H. hermanni, H. albopunctatus, Hypostomus sp. 1, and Hypostomus sp. 2 in the Ivaí River.

Assessing the suitability of mitochondrial and nuclear DNA genetic markers for molecular systematics and species identification of helminths

BACKGROUND

Genetic markers are employed widely in molecular studies, and their utility depends on the degree of sequence variation, which dictates the type of application for which they are suited. Consequently, the suitability of a genetic marker for any specific application is complicated by its properties and usage across studies. To provide a yardstick for future users, in this study we assess the suitability of genetic markers for molecular systematics and species identification in helminths and provide an estimate of the cut-off genetic distances per taxonomic level.

METHODS

We assessed four classes of genetic markers, namely nuclear ribosomal internal transcribed spacers, nuclear rRNA, mitochondrial rRNA and mitochondrial protein-coding genes, based on certain properties that are important for species identification and molecular systematics. For molecular identification, these properties are inter-species sequence variation; length of reference sequences; easy alignment of sequences; and easy to design universal primers. For molecular systematics, the properties are: average genetic distance from order/suborder to species level; the number of monophyletic clades at the order/suborder level; length of reference sequences; easy alignment of sequences; easy to design universal primers; and absence of nucleotide substitution saturation. Estimation of the cut-off genetic distances was performed using the 'K-means' clustering algorithm.

RESULTS

The nuclear rRNA genes exhibited the lowest sequence variation, whereas the mitochondrial genes exhibited relatively higher variation across the three groups of helminths. Also, the nuclear and mitochondrial rRNA genes were the best possible genetic markers for helminth molecular systematics, whereas the mitochondrial protein-coding and rRNA genes were suitable for molecular identification. We also revealed that a general gauge of genetic distances might not be adequate, using evidence from the wide range of genetic distances among nematodes.

CONCLUSION

This study assessed the suitability of DNA genetic markers for application in molecular systematics and molecular identification of helminths. We provide a novel way of analyzing genetic distances to generate suitable cut-off values for each taxonomic level using the 'K-means' clustering algorithm. The estimated cut-off genetic distance values, together with the summary of the utility and limitations of each class of genetic markers, are useful information that can benefit researchers conducting molecular studies on helminths.

Description of a new species and understanding the genetic diversity of Saccocoelioides Szidat, 1954 (Haploporidae) in Middle America using mitochondrial and nuclear DNA sequences

Members of the genus Saccocoelioides Szidat, 1954, include endoparasites from freshwater and brackish fishes from the Americas. Adult specimens were collected from the intestines of Poecilia catemaconis Miller, 1975, a poeciliid fish endemic to Catemaco Lake, and the white mullet Mugil curema Valenciennes, 1836, from Alvarado Lagoon, Veracruz, Mexico. The specimens were sequenced for three molecular markers, internal transcribed spacer 2 (ITS2) and domains D1-D3 from the large subunit (LSU) of nuclear ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) from mitochondrial DNA. The newly sequenced specimens were aligned with other sequences downloaded from GenBank. Maximum likelihood and Bayesian inference analyses were inferred with three data sets (a combination of nuclear DNA ITS2 + LSU, cox 1 alone and the concatenated cox 1+ ITS2 + LSU). The phylogenetic analyses inferred with the combined data set of the two nuclear molecular markers (ITS2 + LSU) revealed that Saccocoelioides is monophyletic and formed 11 independent lineages representing 11 valid species previously recognized plus the new lineage that is herein described as a new species named Saccocoelioides macrospinosus n. sp., however, the new species was placed in a basal polytomy in the tree. Therefore, the addition of a mitochondrial gene with a fast rate of substitution was fundamental to clarify the phylogenetic relationships of the new species. The genetic divergences estimated with the cox 1 gene were high, ranging from 8.3 to 15.5% among Saccocoelioides macrospinosus n. sp. and sister taxa. The new species has a slightly elongated body measuring 440-850 μm long and was classified in the diminutive morphotype. In addition, seven adult specimens recovered from the intestines of the banded tetra fish Astyanax aeneus Günther, 1860 from Nicaragua and Costa Rica formed a monophyletic clade with other specimens identified previously as Saccocoelioides tkachi, expanding its distribution range in other areas of Middle America.