A new nematode species, Bursaphelenchus ussuriensis sp. n. is described in the bark beetle–elm tree association (Scolytus jacobsoni and Ulmus davidiana var. japonica f. suberosa) in the Asian Pacific region of Russia. The new species belongs to the Hofmanni group of Bursaphelenchus and is closest to B. ulmophilus. Its characteristics are as follows: lateral field with three incisures, body length 497–771 µm, post-uterine sac 3.6–5.4 times vulval body diam, 56 (39–66)% of vulva–anus distance, and spicule length 10.3 (9.5–12.5 µm). The new species differs from all species of the Hofmanni group in the closely situated P3 and P4 male caudal papillae and the GP5 small ‘glandpapillae’ pair on the butterfly-like papillae plate, in the set of P1, P2, P3, P4, GP5; vs. in all other species, the P4 papillae pair is absent in the pattern of P1, P2, P3, GP5. The phylogenetic position of B. ussuriensis sp. n. with other species of the Hofmanni group were reconstructed using the D2–D3 expansion segments of 28S and ITS rRNA gene sequence analysis. Sequences of twelve mitochondrial protein-coding genes of B. cocophilus, B. fraudulentus, B. michalskii, B. ussurensis sp. n., and B. willibaldi were obtained in this study. Phylogenetic relationships among eighteen Bursaphelenchus species based on the analysis of the mtDNA sequence dataset are provided and discussed. A modified diagnosis of the Hofmanni group is proposed.

Transposable elements (TEs) comprise a substantial portion of the mammalian genome, with potential implications for both embryonic development and cancer. This study aimed to characterize the expression profiles of TEs in embryonic stem cells (ESCs), cancer cell lines, tumor tissues, and the tumor microenvironment (TME). We observed similarities in TE expression profiles between cancer cells and ESCs, suggesting potential parallels in regulatory mechanisms. Notably, four TE RNAs (HERVH, LTR7, HERV-Fc1, HERV-Fc2) exhibited significant downregulation across cancer cell lines and tumor tissues compared to ESCs, highlighting potential roles in pluripotency regulation. The strong up-regulation of the latter two TEs (HERV-Fc1, HERV-Fc2) in ESCs has not been previously demonstrated and may be a first indication of their role in the regulation of pluripotency. Conversely, tandemly repeated sequences (MSR1, CER, ALR) showed up-regulation in cancer contexts. Moreover, a difference in TE expression was observed between the TME and the tumor bulk transcriptome, with distinct dysregulated TE profiles. Some TME-specific TEs were absent in normal tissues, predominantly belonging to LTR and L1 retrotransposon families. These findings not only shed light on the regulatory roles of TEs in both embryonic development and cancer but also suggest novel targets for anti-cancer therapy. Understanding the interplay between cancer cells and the TME at the TE level may pave the way for further research into therapeutic interventions.

Background: Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered “genomic parasites”, transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. Methods: We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). Results: Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. Conclusions: These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.

Renicolids are parasites of aquatic birds. Their species identification based on morphological characters is problematic. Here, we revised the composition of Renicola spp. parasitising anatids in nearshore areas of northern seas using integrated morphological and molecular data. We redescribed Renicola somateria and verified the diagnosis of R. mediovitellata. We established that the first intermediate host (FIH) of R. somateria is the mollusc Buccinum undatum, while the FIHs of R. mediovitellata are Nucella spp. molluscs. We described the intramolluscan stages of both species. Renicola somateria and R. mediovitellata formed a separate clade in the molecular trees of the Renicolidae. This finding confirms the existence of three main phylogenetic branches of renicolids, differing in the structure of adults, type of cercariae, and host range. Molecular data demonstrated an amphiboreal distribution of both R. somateria and R. mediovitellata. The former is represented by a single population in Europe and the North Pacific, while the latter forms separate populations in these regions. This may be because R. somateria actually uses not only B. undatum but also some other buccinid species with similar circum-Arctic ranges as the FIH. We discuss the roles played in the formation of digenean ranges by the vagility of the definitive host, the lifespan of the adults, and the distribution of the FIH.

Renicolid digeneans parasitize aquatic birds. Their intramolluscan stages develop in marine and brackish-water gastropods, while metacercariae develop in molluscs and fishes. The sys-tematics of renicolids is poorly developed, their life cycles are mostly unknown, and the sta-tuses of many species require revision. Here, we establish based on integrated morphological and molecular data that adult renicolids from gulls Larus argentatus and Larus schistisagus and sporocysts and cercariae of Cercaria parvicaudata from marine snails Littorina spp. are life-cycle stages of the same species. We name it Renicola parvicaudatus and synonymized with it Renicola roscovitus. An analysis of the cox1 gene of R. parvicaudatus from Europe, North America and North Asia demonstrates a low genetic divergence, suggesting that this species has formed quite recently (perhaps during last glacial maximum) and that interregio-nal gene flow is high. In Littorina saxatilis and L. obtusata from the Barents Sea, molecular analysis has revealed intramolluscan stages of Cercaria littorinae saxatilis VIII, a cryptic spe-cies relative to R. parvicaudatus. In the molecular trees, Renicola keimahuri from L. schistisa-gus belongs to another clade than R. parvicaudatus. We show that the species of this clade have cercariae of Rhodometopa group and outline morphological and behavioural transfor-mations leading from xiphidiocercariae to these larvae. Molecular analysis has revealed 3 main phylogenetic branches of renicolids, differing in structure of adults, type of cercariae and host range. Our results elucidate the patterns of host colonization and geographical expansion of renicolids and pave the way to the solution of some long-standing problems of their classification.

Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed.

Digenean larvae of hermaphroditic generation - cercariae - are known to be polymorphic at genetic and behavioural levels. Cercariae arise as a result of parthenogenetic reproduction of intramolluscan stages, and represent a clone if a snail was infected with a single miracidium. Here we investigated cercarial clones of Himasthla elongata - namely, the infectivity of cercariae with normal (negative) and deviant (positive) photoreaction. In our study, most H. elongata clones showed intraclonal variance in their response to light. The proportion of photopositive cercariae ranged between 0.2% and 60% in different H. elongata clones. Photopositive larvae demonstrated significantly reduced rates of encystment in Mytilus edulis haemolymph in vitro and in young mussels. We discuss the possible mechanisms behind intraclonal variations, such as non-specific genomic rearrangements.

We investigated clonal diversity of parthenogenetic larvae, cercaria, with a simplified AFLP (SAFLP, Amplified fragment length polymorphism) method and explored the nature of diverse zones from electrophoretic patterns. LINE retroelements prevail in fragments analized. One of them was aligned to the spacer region in ORF2 of the CR1-like (LINE class) transposon and named CR1-renegade (CR1-rng). CR1-renegade exists in two types of transcripts: the long ones, containing reverse transcriptase and other domains, and the short ones, containing CR1-rng solely. Probes of CR1 reverse transcriptase (CR1-RT) and CR1-rng yielded strikingly different pictures in FISH physical mapping despite being fragments of CR1 transposons. The CR1-RT probe demonstrated dispersed signal distribution throughout the nuclei and all chromosomes while CR1-rng localized preferentially to the heterochromatic regions. We suppose that CR1-rng transcripts are related to lncRNA regulatory network.

Background: Trematodes have a complex life cycle with animal host changes and alternation of parthenogenetic and hermaphrodite generations. The parthenogenetic generation of the worm (rediae) from the first intermediate host Littorina littorea was used for chromosome spreads production. Karyotype description of parasitic flatworm Himasthla elongata Mehlis, 1831 (Digenea: Himasthlidae) based on fluorochrome banding and 18S rDNA mapping.Results: Chromosome spreads were obtained from cercariae embryos and redial tissue suspensions with high pressure squash method. 74.4 % of the analysed spreads contained 12 chromosome pairs (2n = 24). Chromosome classification was performed according to the morphometry and nomenclature published. H. elongata spread chromosomes had a rather bead-like structure. Ideograms of DAPI-banded chromosomes contained 130 individual bands. According to flow cytometry data, the H. elongata genome contains 1.25 pg of DNA, so one band contains, on average, 9.4 Mb of DNA. Image bank captures of individual high-resolution DAPI-banded chromosomes were provided. Differential DAPI- and CMA(3)-staining revealed the chromatin areas that differed in AT-or GC-content. Both dyes stained chromosomes all along but with varying intensities in different areas. FISH revealed that vast majority (95.0 %) of interphase nuclei contained one signal for 18S rDNA. This corresponded to the number of nucleoli per cell detected by observations in vivo. The rDNA signal was observed on one or two homologs of chromosome 10 in 72.2 % of analysed chromosome spreads, therefore chromosome 10 possessed the main rDNA cluster and minor ones on chromosomes 3 and 6, that corresponds with AgNOR results.Conclusions: Himasthla elongata chromosomes variations presented as image bank. Differential chromosome staining with fluorochromes and FISH used for 18S rDNA mapping let us to conclude: (1) Himasthla elongata karyotype is 2n = 24; (2) chromosome number deviates from the previously studied echinostomatids (2n = 14-22); (3). Chromosome 10 possesses the main rDNA cluster with the minor ones existing on chromosomes 3 and 6.

We cloned and analyzed Hemar1-the full-length mariner of Himasthla elongata. Hemar1 amount and distribution in the genome is typical for the transposable elements. Hemar1 closest relatives found in databases are the mariner-like element (MLE) of Girardia tigrina with 88% similarity in the most conserved transposase domain and Cemar1 of Caenorhabditis elegans with the most similar inverted terminal repeats. Hydra's (Cnidaria) MLE are the next in similarity to Hemar1. We checked whether sequences similar to Hemar1 exist in intermediate and definitive hosts of the parasitic trematode and did not find obvious similarity. This fact, together with the data of Hemar1 evolutionary position, argues against recent MLE-mediated horizontal transfer in this parasite-host model. Our results demonstrate that H. elongata generates genomic variability in asexual parthenogenetic generations within the snail. Transposon insertional display based on full-length sequence showed that Hemar1 could be located in the regions involved in generating clonal diversity in rediae and cercariae, that is, trematode parthenitae.