Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation

Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa)

Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.

A new Ceratomyxa (Cnidaria: Myxosporea) infecting the ornamental fish species Pterophyllum scalare from the Amazon Region, Brazil

A new parasite of the Class Myxozoa is described in the gallbladder of the ornamental angelfish Pterophyllum scalare, in two municipalities in the state of Amapá, Brazil, based on morphological, morphometric and phylogenetic descriptions. From October 2022 to August 2024 fifty-five angelfish specimens were sampled in Macapá (n=10) and Tartarugalzinho (n=45). Slightly arched mixospores were observed by light microscopy and had characteristics consistent with those of the genus Ceratomyxa. These obtained an average length of 1.6 ± 0.2 µm and 11.5 ± 1.1 µm in thickness. The polar capsules were subspherical and 0.7 ± 0.1 µm long and 0.6 ± 0.1 µm wide, with 3 to 4 turns of the polar filament. Phylogenetic analysis showed that the new species is grouped in the family Ceratomyxidae, in addition to being positioned in the same subclade of freshwater ceratomyxids from the Brazilian Amazon, demonstrating that this species shares a common ancestor with its close relatives, based on geographic affinity. Ceratomyxa tavariensis n. sp. is the first species of the class Myxozoa described infecting angelfish in Brazil, and the thirteenth species of Ceratomyxa described in the country.

Histopathological and phylogenetic description of an Amazonian cnidaria microparasite Myxobolus rousseauxii n. sp. infecting the gill arches of Brachyplatystoma rousseauxii (Siluriformes)

From genus Myxobolus, cnidarians of Myxozoa class, is well known for infecting economically important fish species and, as result, relevant losses in aquaculture production can be observed. They are present in a big range of fish in its natural habitat, including the migratory Brachyplatystoma rousseauxii catfish. This study aimed is to develop an integrative characterization of a new species of Myxobolus, located in B. rousseauxii's gills. To accomplish this, 30 specimens of B. rousseauxii catfish were collected from Mosqueiro Island in Pará, Brazil; necropsied and analyzed for morphology, histology and molecular characteristics. Cysts with conjunctival capsule development made up of fibroblasts were observed at the gill arches; such proliferation caused bone tissue loss and cartilage compression. The cysts contained Myxobolus myxospores measuring 9.9 μm of length and 9.6 μm of width, whereas polar capsules were 5.4 μm long and 3.4 μm wide, with 8 to 9 coils of polar tubules. Phylogenetic analyses revealed that new species were included in a subclade alongside species from the same geographic location and infection site that infect Siluriformes fish. Morphological and molecular differences revealed that Myxobolus spp. parasite-host associations through histopathology supporting the designation of a new M. rousseauxii n. sp. species in B. rousseauxii, a commercially important fish.

A Gallbladder Ceratomyxidae (Myxozoa: Bivalvulida) Parasite Described In Pimelodella cristata (Müller & Troschel, 1848) From the Eastern Amazon

PURPOSE

The Myxozoa class is characterized by parasites that have valves joined by a suture line and polar capsules containing eversible spiral filamento and this class is considered an obligate parasite. The genus Ceratomyxa has approximately 300 species described in fish, both marine and freshwater fish, mainly infecting the gallbladder, but also occurring in the urinary bladder. This study describes a new species of Ceratomyxa in the Amazon region for Pimelodella cristata.

METHODS

For these analyses, the fish were desensitized by means of a medullary section with the aid of a sharp metallic instrument. With the fish desensitized, the entire body surface was examined under a binocular stereoscopic microscope. The gallbladder fragments were collected and fixed in Davidson for histological analyses and in ethanol for molecular analyses.

RESULTS

This parasite was found in the host's gallbladder, with elongated spores in a decreasing shape in sutural view, measuring 1.64 ± 0.6 μm in length and 17.13 ± 2.6 μm in width. The polar capsules had a spherical shape of equal size and measured 1.36 ± 0.17 μm in length and 0.9 ± 0.05 μm in width, and each polar capsule contained 4 to 5 turns.

CONCLUSION

Morphological and phylogenetic analyzes denote that this is a new species of the genus Ceratomyxa.

A new myxozoan parasitizing Mesonauta festivus (Cichliformes: Cichlidae) from the lake region in the municipality of Tartarugalzinho, Eastern Amazon, Brazil

The Amazon is the largest river basin in the world and it is home to the greatest diversity of freshwater fish in the world. Mesonauta festivus is a cichlid popularly known as flag cichlid, widely distributed throughout South America. The diversity of parasites in fish from the Amazon region is still underestimated, due to the high fishes diversity. The Myxozoa class has a universal distribution, with some specimens being pathogenic to some fish. The aim of this work was to describe a new species of Hoferellus in M. festivus. The fish were collected in the lake region, municipality of Tartarugalzinho, in the state of Amapá, Brazil. The new species was found parasitizing the urinary bladder of M. festivus. Spores were 11.5 ±1.1 (10.4-12.6) µm long and 10.9 ±1 (9.9-11.9) µm wide, and polar capsules were equally sized, measuring 4.9 ±0.5 (4.4-5.4) µm long and 3.4 ±0.9 (2.5-4.3) µm wide, with a pyriform shape, convergent with the apical region of the spore. The polar filament was wound with 5 to 6 turns. Morphological, morphometric, molecular and phylogenetic analysis proved that it is a new species of Hoferellus in the Amazon region.

Ceratomyxa matosi n. sp. (Myxozoa: Ceratomyxidae) parasitizing the gallbladder of Boulengerella cuvieri (Characiformes: Ctenoluciidae) State of Amapá, Brazilian Amazon

Myxozoa is a class of the Phylum Cnidaria made up of endoparasites from aquatic habitats. The genus Ceratomyxa preferentially infects marine fish, with the gallbladder being the main site parasitized. This study aimed to describe a new species of Ceratomyxa found in this organ in Boulengerella cuvieri using morphological, morphometric characterization and phylogenetic analysis of 18S rDNA gene sequences. Specimens of B. cuvieri were collected, anesthetized, desensitized and biometric measurements were performed. The organs were analyzed under a stereomicroscope and fragments of internal organs were extracted for light microscopy analysis, preserved in 80% ethanol for 18S rDNA gene analysis and fixed in Davidson solution for histological processing. Free spores of Ceratomyxa were observed in the gallbladder, in plasmodia with wave-like movements, with the following dimensions: spore width (24.5 ± 0.4) µm, spore length (5.2 ± 0.3) µm, polar capsule width (1.8 ± 0.2) µm, polar capsule length (2.1 ± 0.3) µm, number of polar tubule turns (4-5) and 100% prevalence. Phylogenetic analysis confirmed that Ceratomyxa matosi n. sp. is a new species, grouped with other freshwater Ceratomyxa species from the Amazon, representing the second description of species of this genus in the state of Amapá.

Henneguya patriciai n. sp. (Cnidaria: Myxosporea) parasitizing Leporinus friderici (Bloch 1794) from Tartarugalzinho river, eastern Amazon

The Amazon basin has the largest number of fish in the world, and among the most common fishes of the Neotropical region, the threespot (Leporinus friderici) is cited, which in relation to its microparasitic fauna, has described only 1 species of the genus Henneguya, Henneguya friderici. The Myxozoa class is considered an obligate parasite, being morphologically characterized by spores formed by valves connected by a suture line. This study describes a new species of Henneguya sp. in the Amazon region for L. friderici. This parasite was found in the host's pyloric caeca and caudal kidney, with mature spores with a total spore length of 38.4 ± 2.5 (35.9–40.9) μm; the spore body 14.4 ± 1.1 (13.3–15.5) μm and 7.3 ± 0.6 (6.7–7.9) μm wide. Regarding its 2 polar capsules, they had a length of 5.1 ± 0.4 (4.7–5.5) μm and a width of 2.0 ± 0.1 (1.9–2.1) μm in the same pear-shaped, and each polar capsule contained 9–11 turns. Morphological and phylogenetic analyses denote that this is a new species of the genus Henneguya.

Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases

5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.

Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases

5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.

Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing

A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.

A myxozoan genome reveals mosaic evolution in a parasitic cnidarian

BACKGROUND

Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functions of parasitism in some parasite genomes, reminiscent of widespread mosaic evolution-where subregions of a genome have different rates of evolutionary change. We found evidence of mosaic genome evolution in the cnidarian Myxobolus honghuensis, a myxozoan parasite of fish, with extremely simple morphology.

RESULTS

We compared M. honghuensis with other myxozoans and free-living cnidarians, and determined that it has a relatively larger myxozoan genome (206 Mb), which is less reduced and less compact due to gene retention, large introns, transposon insertion, but not polyploidy. Relative to other metazoans, the M. honghuensis genome is depleted of neural genes and has only the simplest animal immune components. Conversely, it has relatively more genes involved in stress resistance, tissue invasion, energy metabolism, and cellular processes compared to other myxozoans and free-living cnidarians. We postulate that the expansion of these gene families is the result of evolutionary adaptations to endoparasitism. M. honghuensis retains genes found in free-living Cnidaria, including a reduced nervous system, myogenic components, ANTP class Homeobox genes, and components of the Wnt and Hedgehog pathways.

CONCLUSIONS

Our analyses suggest that the M. honghuensis genome evolved as a mosaic of conservative, divergent, depleted, and enhanced genes and pathways. These findings illustrate that myxozoans are not as genetically simple as previously regarded, and the evolution of some myxozoans is driven by both genomic streamlining and expansion.

The role of DNA methylation in genome defense in Cnidaria and other invertebrates

Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.

OUP accepted manuscript

DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.

Epigenetic Regulation in Hydra: Conserved and Divergent Roles

Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for >250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on Hydra spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, Hydra exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in Hydra with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in Hydra, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of Hydra.

Neural versus alternative integrative systems: molecular insights into origins of neurotransmitters

Transmitter signalling is the universal chemical language of any nervous system, but little is known about its early evolution. Here, we summarize data about the distribution and functions of neurotransmitter systems in basal metazoans as well as outline hypotheses of their origins. We explore the scenario that neurons arose from genetically different populations of secretory cells capable of volume chemical transmission and integration of behaviours without canonical synapses. The closest representation of this primordial organization is currently found in Placozoa, disk-like animals with the simplest known cell composition but complex behaviours. We propose that injury-related signalling was the evolutionary predecessor for integrative functions of early transmitters such as nitric oxide, ATP, protons, glutamate and small peptides. By contrast, acetylcholine, dopamine, noradrenaline, octopamine, serotonin and histamine were recruited as canonical neurotransmitters relatively later in animal evolution, only in bilaterians. Ligand-gated ion channels often preceded the establishment of novel neurotransmitter systems. Moreover, lineage-specific diversification of neurotransmitter receptors occurred in parallel within Cnidaria and several bilaterian lineages, including acoels. In summary, ancestral diversification of secretory signal molecules provides unique chemical microenvironments for behaviour-driven innovations that pave the way to complex brain functions and elementary cognition. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

Advances and Discoveries in Myxozoan Genomics

Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first 'omic' datasets have now become the main resource for a better understanding of host-parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data.