Chromosome-level genome assembly of Hydractinia symbiolongicarpus

Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes

Despite the striking conservation of animal chromosomes, their repetitive element complements are vastly diverse. Only recently, high quality chromosome-level genome assemblies enabled identification of repeat compositions along a broad range of animal chromosomes. Here, utilizing the chromosome-level genome assembly of Hydractinia symbiolongicarpus, a colonial hydrozoan cnidarian, we describe an accumulation of a single 372 bp repeat unit in the subtelomeric regions. Based on the sequence divergence, its partial affinity with the Helitron group can be detected. This sequence is associated with a repeated minisatellite unit of about 150 bp. Together, they account for 26.1% of the genome (126 Mb of the 483 Mb). This could explain the genome size increase observed in H. symbiolongicarpus compared with other cnidarians, yet distinguishes this expansion from other large cnidarian genomes, such as Hydra vulgaris, where such localized propagation is absent. Additionally, we identify a derivative of an IS3EU-like DNA element accumulated at the putative centromeric regions. Our analysis further reveals that Helitrons generally comprise a large proportion of H. symbiolongicarpus (11.8%). We investigated Helitron presence and distributions across several cnidarian genomes. We find that in Nematostella vectensis, an anthozoan cnidarian, Helitron-like sequences were similarly accumulated at the subtelomeric regions. All these findings suggest that Helitron derivatives are prone to forming chromosomal extensions in cnidarians through local amplification in subtelomeric regions, driving variable genome expansions within the clade.

The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality

Coloniality is a widespread growth form in cnidarians, tunicates, and bryozoans, among others. Colonies function as single physiological units despite their modular structure of zooids and supporting tissues. A key question is how structurally and functionally distinct colony parts are generated. In the cnidarian Hydractinia symbiolongicarpus, colonies consist of zooids (polyps) interconnected by stolons attached to the substrate. Using single-cell transcriptomics, we profiled ~200,000 Hydractinia cells, including stolons and two polyp types, identifying major cell types and their distribution across colony parts. Distinct colony parts are primarily characterised by unique combinations of shared cell types and to a lesser extent by part-specific cell types. We identified cell type-specific transcription factors (TFs) and gene sets expressed within these cell types. This suggests that cell type combinations and occasional innovations drive the evolution of coloniality in cnidarians. We uncover a novel stolon-specific cell type linked to biomineralization and chitin synthesis, potentially crucial for habitat adaptation. Additionally, we describe a new cell type mediating self/non-self recognition. In summary, the Hydractinia cell atlas provides insights into the cellular and molecular mechanisms underpinning coloniality.

The Chromosome-level Genome of the Ctenophore Mnemiopsis leidyi A. Agassiz, 1865 Reveals a Unique Immune Gene Repertoire

Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one of the most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly of M. leidyi with a focus on its immune gene repertoire. The genome was 247.97 Mb, with N50 16.84 Mb, and 84.7% completeness. Its karyotype was 13 chromosomes. In this genome and that of two other ctenophores, Bolinopsis microptera and Hormiphora californensis, we detected a high number of protein domains related to potential immune receptors. Among those, proteins containing Toll/interleukin-1 (TIR2) domain, NACHT domain, Scavenger Receptor Cystein-Rich (SRCR) domain, or C-type Lectin domain (CTLD) were abundant and presented unique domain architectures in M. leidyi. M. leidyi seems to lack bona fide Toll-like Receptors, but it does possess a repertoire of 15 TIR2 domain-containing genes. Besides, we detected a bona fide NOD-like receptor and 38 NACHT domain-containing genes. In order to verify the function of those domain-containing genes, we exposed M. leidyi to the pathogen Vibrio coralliilyticus. Among the differentially expressed genes, we identified potential immune receptors, including four TIR2 domain-containing genes, all of which were upregulated in response to pathogen exposure. To conclude, many common immune receptor domains, highly conserved across metazoans, are already present in Ctenophora. These domains have large expansions and unique architectures in M. leidyi, findings consistent with the basal evolutionary position of this group, but still might have conserved functions in immunity and host-microbe interaction.

Molecular evolution of ovothiol biosynthesis in animal life reveals diversity of the natural antioxidant ovothiols in Cnidaria

Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs. In this work, we have integrated genome and transcriptome mining with biochemical analyses to study the evolution and diversification of OSHs biosynthesis in cnidarians. By tracing the history of the ovoA gene, we inferred its loss in the latest common ancestor of Medusozoa, followed by the acquisition of a unique ovoB/ovoA chimaeric gene in Hydrozoa, likely through a horizontal gene transfer from dinoflagellate donors. While Anthozoa (corals and anemones), bearing canonical ovoA genes, produced a striking variety of OSHs (A, B, and C), the multifunctional enzyme in Hydrozoa was related to OSH B biosynthesis, as shown in Clytia hemisphaerica. Surprisingly, the ovoA-lacking jellyfish Aurelia aurita and Pelagia noctiluca also displayed OSHs, and we provided evidence of their incorporation from external sources. Finally, transcriptome mining revealed ovoA conserved expression pattern during larval development from Cnidaria to more evolved organisms and its regulation by external stimuli, such as UV exposure. The results of our study shed light on the origin and diversification of OSH biosynthesis in basal animals and highlight the importance of redox-active molecules from ancient metazoans as cnidarians to vertebrates.

Apoptosis-dependent head development during metamorphosis of the cnidarian Hydractinia symbiolongicarpus

Apoptosis is a regulated cell death that depends on caspases. It has mainly been studied as a mechanism for the removal of unwanted cells. However, apoptotic cells can induce fate or behavior changes of their neighbors and thereby participate in development. Here, we address the functions of apoptosis during metamorphosis of the cnidarian Hydractinia symbiolongicarpus. We describe the apoptotic profile during metamorphosis of the larva and identify Caspase3/7a, but no other executioner caspases, as essential for apoptosis in this context. Using pharmacological and genetic approaches, we find that apoptosis is required for normal head development. Inhibition of apoptosis resulted in defects in head morphogenesis. Neurogenesis was compromised in the body column of apoptosis-inhibited animals but there was no effect on the survival or proliferation of stem cells, suggesting that apoptosis is required for cellular commitment rather than for the maintenance of their progenitors. Differential transcriptomic analysis identifies TRAF genes as downregulated in apoptosis-inhibited larvae and functional experiments provide evidence that they are essential for head development. Finally, we find no major role for apoptosis in head regeneration in this animal, in contrast to the significance of apoptosis in Hydra head regeneration.

Novel technologies uncover novel 'anti'-microbial peptides in Hydra shaping the species-specific microbiome

The freshwater polyp Hydra uses an elaborate innate immune machinery to maintain its specific microbiome. Major components of this toolkit are conserved Toll-like receptor (TLR)-mediated immune pathways and species-specific antimicrobial peptides (AMPs). Our study harnesses advanced technologies, such as high-throughput sequencing and machine learning, to uncover a high complexity of the Hydra's AMPs repertoire. Functional analysis reveals that these AMPs are specific against diverse members of the Hydra microbiome and expressed in a spatially controlled pattern. Notably, in the outer epithelial layer, AMPs are produced mainly in the neurons. The neuron-derived AMPs are secreted directly into the glycocalyx, the habitat for symbiotic bacteria, and display high selectivity and spatial restriction of expression. In the endodermal layer, in contrast, endodermal epithelial cells produce an abundance of different AMPs including members of the arminin and hydramacin families, while gland cells secrete kazal-type protease inhibitors. Since the endodermal layer lines the gastric cavity devoid of symbiotic bacteria, we assume that endodermally secreted AMPs protect the gastric cavity from intruding pathogens. In conclusion, Hydra employs a complex set of AMPs expressed in distinct tissue layers and cell types to combat pathogens and to maintain a stable spatially organized microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Hydractinia is a colonial marine hydroid that shows remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, Hydractinia symbiolongicarpus and Hydractinia echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell-type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from nonself.

Web of venom: exploration of big data resources in animal toxin research

Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.