Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)

Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata

Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including Hydra and the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with the fact that spawning can be induced in the laboratory, during the reproductive window, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research.

Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library

BACKGROUND

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these sequences remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) in a phylogenetic context. We sequenced and assembled de novo the genome of Actinostella flosculifera and analyzed a total of 38 nuclear genomes to create the first ActiniariaREP library (Actiniaria-REPlib). We compared Actiniaria-REPlib with Repbase and RepeatModeler2 libraries, and used dnaPipeTE to annotate REPs from genomic short-read datasets of 36 species for divergence landscapes.

RESULTS

Our study assembled and annotated the mitochondrial genomes, including 27 newly assembled ones. We re-annotated ~92% of the unknown sequences from the initial nuclear genome library, finding that 6.4-30.6% were DNA transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, and 1.2-7% unclassifiable sequences. Actiniaria-REPlib recovered 9.4x more REP sequences from actiniarian genomes than Dfam and 10.4x more than Repbase. It yielded 79,903 annotated TE consensus sequences (74,643 known, 5,260 unknown), compared to Dfam with 7,697 (3,742 known, 3,944 unknown) and Repbae (763 known).

CONCLUSIONS

Our study significantly enhances the characterization of sea anemone repetitive DNA, assembling mitochondrial genomes, re-annotating nuclear sequences, and identifying diverse repeat elements. Actiniaria-REPlib vastly outperforms existing databases, recovering significantly more REP sequences and providing a comprehensive resource for future genomic and evolutionary studies in Actiniaria.

Genomic comparison of the temperate coral Astrangia poculata with tropical corals yields insights into winter quiescence, innate immunity, and sexual reproduction

Facultatively symbiotic corals provide important experimental models to explore the establishment, maintenance, and breakdown of the mutualism between corals and members of the algal family Symbiodiniaceae. Here, we report the de novo chromosome-scale genome assembly and annotation of the facultatively symbiotic, temperate coral Astrangia poculata. Though widespread segmental/tandem duplications of genomic regions were detected, we did not find strong evidence of a whole-genome duplication event. Comparison of the gene arrangement between As. poculata and the tropical coral Acropora millepora revealed considerable conserved colinearity despite ∼415 million years of divergence. Gene families related to sperm hyperactivation and innate immunity, including lectins, were found to contain more genes in Ac. millepora relative to As. poculata. Sperm hyperactivation in Ac. millepora is expected given the extreme requirements of gamete competition during mass spawning events in tropical corals, while lectins are important in the establishment of coral-algal symbiosis. By contrast, gene families involved in sleep promotion, feeding suppression, and circadian sleep/wake cycle processes were expanded in As. poculata. These expanded gene families may play a role in As. poculata's ability to enter a dormancy-like state (winter quiescence) to survive freezing temperatures at the northern edges of the species' range.

De novo genome assembly of the Edwardsiid anthozoan Edwardsia elegans

Cnidarians (sea anemones, corals, hydroids, and jellyfish) are a key outgroup for comparisons with bilateral animals to trace the evolution of genomic complexity and diversity within the animal kingdom, as they separated from most other animals 100 s of million years ago. Cnidarians have extensive diversity, yet the paucity of genomic resources limits our ability to compare genomic variation between cnidarian clades and species. Here, we report the genome for Edwardsia elegans, a sea anemone in the most specious genus of the family Edwardsiidae, a phylogenetically important family of sea anemones that contains the model anemone Nematostella vectensis. The E. elegans genome is 396 Mb in length and is predicted to encode approximately 49,000 proteins. We annotated a large conservation of macrosynteny between E. elegans and other Edwardsiidae anemones as well as conservation of both microRNAs and ultra-conserved noncoding elements previously reported in other cnidarians species. We also highlight microsyntenic variation of clustered developmental genes and ancient gene clusters that vary between species of sea anemones, despite previous research showing conservation between cnidarians and bilaterians. Overall, our analysis of the E. elegans genome highlights the importance of using multiple species to represent a taxonomic group for genomic comparisons, where genomic variation can be missed for large and diverse clades.

Unveiling the early evolution of black corals

Black corals, primarily deep-sea cnidarians (Anthozoa: Antipatharia), are inferred to have originated either in the Ediacaran or Cambrian based on molecular clock estimates. However, only the fossil family Sinopathidae, comprising Sinopathes and Sterictopathes, from the Early Ordovician of Hubei, China, has been recorded in the fossil record. The affinity of this family has been questioned because of morphological inconsistencies between fossil and extant species. Here we describe two transitional species of Sterictopathes from the Middle Ordovician of Shaanxi, China, bridging the fossil gaps and thereby elevating the genus Sterictopathes to a new family, Sterictopathidae fam. nov. The hypothesized evolutionary trend toward regularity in the axial skeleton from the Ordovician to modern Antipatharia is highlighted by reduced ridges and longitudinal fusion of networks. This discovery and confirmation of Ordovician black corals paves the way for future fossil findings and offers new insights into the early evolution of Hexacorallia.

Depth-structured lineages in the coral Stylophora pistillata of the Northern Red Sea

Coral reefs are biodiversity hotspots, where new species continue to be discovered. Stylophora pistillata, a depth-generalist coral, is widely distributed throughout the Indo-Pacific and has long been considered the poster child for phenotypic plasticity. It occupies a wide range of reef habitats and exhibits a myriad of gross morphologies. Here, we used reduced representation genome sequencing (nextRAD) to assess the genetic structure of adults and recruits of S. pistillata across shallow and mesophotic populations in the northern Red Sea (Gulf of Aqaba). Across analytical approaches, we observed a complex genetic structure with at least four genetically divergent lineages occurring sympatrically with little to no admixture and structured by depth. Morphological and physiological differences previously documented suggest that the long-considered ecological opportunism of S. pistillata in the Red Sea may, in fact, have a genetic basis. Assessment of both adult colonies and recruits within each of the lineages also revealed the prevalence of local recruitment and genetic structuring across the eight-kilometer section of the Israeli Red Sea coastline. Overall, the observed patterns confirm the presence of undescribed diversity within this model organism for coral physiology and corroborate a broader pattern of extensive undescribed diversity within scleractinian corals.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

The proteotranscriptomic characterization of venom in the white seafan Eunicella singularis elucidates the evolution of Octocorallia arsenal

All the members of the phylum Cnidaria are characterized by the production of venom in specialized structures, the nematocysts. Venom of jellyfish (Medusozoa) and sea anemones (Anthozoa) has been investigated since the 1970s, revealing a remarkable molecular diversity. Specifically, sea anemones harbour a rich repertoire of neurotoxic peptides, some of which have been developed in drug leads. However, venoms of the vast majority of Anthozoa species remain uncharacterized, particularly in the class Octocorallia. To fill this gap, we applied a proteo-transcriptomic approach to investigate venom composition in Eunicella singularis, a gorgonian species common in Mediterranean hard-bottom benthic communities. Our results highlighted the peculiarities of the venom of E. singularis with respect to sea anemones, which is reflected in the presence of several toxins with novel folds, worthy of functional characterization. A comparative genomic survey across the octocoral radiation allowed us to generalize these findings and provided insights into the evolutionary history, molecular diversification patterns and putative adaptive roles of venom toxins. A comparison of whole-body and nematocyst proteomes revealed the presence of different cytolytic toxins inside and outside the nematocysts. Two instances of differential maturation patterns of toxin precursors were also identified, highlighting the intricate regulatory pathways underlying toxin expression.

Proteomic Diversity of the Sea Anemone Actinia fragacea: Comparative Analysis of Nematocyst Venom, Mucus, and Tissue-Specific Profiles

Sea anemones (Actiniaria, Cnidaria) are promising targets for biomedical research, as they produce unique bioactive compounds, including toxins and antimicrobial peptides (AMPs). However, the diversity and mechanisms underlying their chemical defenses remain poorly understood. In this study, we investigate the proteomic profiles of the unexplored sea anemone Actinia fragacea by analyzing its venom nematocyst extract, tissues, and mucus secretion. A total of 4011 different proteins were identified, clustered into 3383 protein groups. Among the 83 putative toxins detected, actinoporins, neurotoxins, and phospholipase A2 were uncovered, as well as two novel zinc metalloproteinases with two specific domains (ShK) associated with potassium channel inhibition. Common Gene Ontology (GO) terms were related to immune responses, cell adhesion, protease inhibition, and tissue regeneration. Furthermore, 1406 of the 13,276 distinct peptides identified were predicted as potential AMPs, including a putative Aurelin-like AMP localized within the nematocysts. This discovery highlights and strengthens the evidence for a cnidarian-exclusive Aurelin peptide family. Several other bioactive compounds with distinctive defense functions were also detected, including enzymes, pattern recognition proteins (PRPs), and neuropeptides. This study provides the first proteome map of A. fragacea, offering a critical foundation for exploring novel bioactive compounds and valuable insights into its molecular complexity.

Unlocking Antimicrobial Peptides: In Silico Proteolysis and Artificial Intelligence-Driven Discovery from Cnidarian Omics

Overcoming the growing challenge of antimicrobial resistance (AMR), which affects millions of people worldwide, has driven attention for the exploration of marine-derived antimicrobial peptides (AMPs) for innovative solutions. Cnidarians, such as corals, sea anemones, and jellyfish, are a promising valuable resource of these bioactive peptides due to their robust innate immune systems yet are still poorly explored. Hence, we employed an in silico proteolysis strategy to search for novel AMPs from omics data of 111 Cnidaria species. Millions of peptides were retrieved and screened using shallow- and deep-learning models, prioritizing AMPs with a reduced toxicity and with a structural distinctiveness from characterized AMPs. After complex network analysis, a final dataset of 3130 Cnidaria singular non-haemolytic and non-toxic AMPs were identified. Such unique AMPs were mined for their putative antibacterial activity, revealing 20 favourable candidates for in vitro testing against important ESKAPEE pathogens, offering potential new avenues for antibiotic development.

The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses

The ability of octocorals and stony corals to deposit calcium carbonate (CaCO3) has contributed to their ecological success. Whereas stony corals possess a homogeneous aragonite skeleton, octocorals have developed distinct skeletal structures composed of different CaCO3 polymorphs and a skeletal organic matrix. Nevertheless, the molecular basis of skeletal structure formation in octocorals remains inadequately understood. Here, we sequenced the genomes and skeletal proteomes of two calcite-forming octocorals, namely Paragorgia papillata and Chrysogorgia sp. The assembled genomes sizes were 618.13 Mb and 781.04 Mb for P. papillata and Chrysogorgia sp., respectively, with contig N50s of 2.67 Mb and 2.61 Mb. Comparative genomic analyses identified 162 and 285 significantly expanded gene families in the genomes of P. papillata and Chrysogorgia sp., respectively, which are primarily associated with biomineralization and immune response. Furthermore, comparative analyses of skeletal proteomes demonstrated that corals with different CaCO3 polymorphs share a fundamental toolkit comprising cadherin, von Willebrand factor type A, and carbonic anhydrase domains for calcified skeleton deposition. In contrast, collagen is abundant in the calcite-forming octocoral skeletons but occurs rarely in aragonitic stony corals. Additionally, certain collagens have developed domains related to matrix adhesion and immunity, which may confer novel genetic functions in octocoral calcification. These findings enhance our understanding of the diverse forms of coral biomineralization processes and offer preliminary insights into the formation and evolution of the octocoral skeleton.

A faunal inventory of methane seeps on the Pacific margin of Costa Rica

The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300-3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also reported for species known from Mexico, the Galápagos seamounts, Chile, and the western Pacific; as well as 16 new depth records and three new seep records for species known to occur at vents or organic falls. No single evolutionary narrative explains the patterns of biodiversity at these seeps, as even morphologically indistinguishable species can show different biogeographic affinities, biogeographic ranges, or depth ranges. The value of careful molecular taxonomy and comprehensive specimen-based regional inventories is emphasized for biodiversity research and monitoring.

Genome sequence of the Mediterranean red coral Corallium rubrum

OBJECTIVES

Corallium rubrum, the precious red coral, is an octocoral endemic to the western Mediterranean Sea. Like most octocorals, it produces tiny, calcified structures called sclerites. Uniquely, it also produces a completely calcified axial skeleton that is a bright red color. This combination of color and hardness has made the red coral prized for centuries, leading to extensive fishing and trade for use in jewelry. Understanding how it produces this red skeleton is thus a central question in economics, culture, and biology. To gain insights into this process, we sequenced the C. rubrum genome.

DATA DESCRIPTION

Our C. rubrum genome assembly is 655 megabases (Mb) in size, distributed across 2910 scaffolds with a very low level of unknown nucleotides (0.95%). We used a pipeline based on the MaSuRCA hybrid assembler, combining long PacBio reads and short Illumina reads, followed by several steps to improve the assembly, including scaffolding, merging, and polishing. This represents the third published genome of an octocoral and the first within the order Scleralcyonacea.

Coral photosymbiosis on Mid-Devonian reefs

The ability of stony corals to thrive in the oligotrophic (low-nutrient, low-productivity) surface waters of the tropical ocean is commonly attributed to their symbiotic relationship with photosynthetic dinoflagellates1,2. The evolutionary history of this symbiosis might clarify its organismal and environmental roles3, but its prevalence through time, and across taxa, morphologies and oceanic settings, is currently unclear4-6. Here we report measurements of the nitrogen isotope (15N/14N) ratio of coral-bound organic matter (CB-δ15N) in samples from Mid-Devonian reefs (Givetian, around 385 million years ago), which represent a constraint on the evolution of coral photosymbiosis. Colonial tabulate and fasciculate (dendroid) rugose corals have low CB-δ15N values (2.51 ± 0.97‰) in comparison with co-occurring solitary and (pseudo)colonial (cerioid or phaceloid) rugose corals (5.52 ± 1.63‰). The average of the isotopic difference per deposit (3.01 ± 0.58‰) is statistically indistinguishable from that observed between modern symbiont-barren and symbiont-bearing corals (3.38 ± 1.05‰). On the basis of this evidence, we infer that Mid-Devonian tabulate and some fasciculate (dendroid) rugose corals hosted active photosymbionts, while solitary and some (pseudo)colonial (cerioid or phaceloid) rugose corals did not. The low CB-δ15N values of the Devonian tabulate and fasciculate rugose corals relative to the modern range suggest that Mid-Devonian reefs formed in biogeochemical regimes analogous to the modern oligotrophic subtropical gyres. Widespread oligotrophy during the Devonian may have promoted coral photosymbiosis, the occurrence of which may explain why Devonian reefs were the most productive reef ecosystems of the Phanerozoic.

Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals

Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species.

Sea anemone (Anthozoa, Actiniaria) diversity in Mo'orea (French Polynesia)

Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.

Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment

The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.

The Palaeobiology of Two Crown Group Cnidarians: Haootia quadriformis and Mamsetia manunis gen. et sp. nov. from the Ediacaran of Newfoundland, Canada

The Ediacaran of eastern Newfoundland preserves the world's oldest known eumetazoan body fossils, as well as the earliest known record of fossilized muscular tissue. Re-examination of the holotype of the eight-armed Haootia quadriformis in terms of its morphology, the arrangement of its muscle filament bundles, and hitherto undescribed aspects of its anatomy support its interpretation as a crown staurozoan. We also document several new fossils preserving muscle tissue with a different muscular architecture to Haootia, but with only four arms. This new material allows us to describe a new crown group staurozoan, Mamsetia manunis gen. et sp. nov. This work confirms the presence of crown group medusozoan cnidarians of the Staurozoa in the Ediacaran of Newfoundland circa 565 Ma.

From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae)

In this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily's ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00338-024-02537-1.

The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution

The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes.

Microbiome manipulation by corals and other Cnidaria via quorum quenching

A dynamic mucous layer containing numerous micro-organisms covers the surface of corals and has multiple functions including both removal of sediment and "food gathering."1 It is likely to also act as the primary barrier to infection; various proteins and compounds with antimicrobial activity have been identified in coral mucus, though these are thought to be largely or exclusively of microbial origin. As in Hydra,2 anti-microbial peptides (AMPs) are likely to play major roles in regulating the microbiomes of corals.3,4 Some eukaryotes employ a complementary but less obvious approach to manipulate their associated microbiome by interfering with quorum signaling, effectively preventing bacteria from coordinating gene expression across a population. Our investigation of immunity in the reef-building coral Acropora millepora,5 however, led to the discovery of a coral gene referred to here as AmNtNH1 that can inactivate a range of acyl homoserine lactones (AHLs), common bacterial quorum signaling molecules, and is induced on immune challenge of adult corals and expressed during the larval settlement process. Closely related proteins are widely distributed within the Scleractinia (hard corals) and some other cnidarians, with multiple paralogs in Acropora, but their closest relatives are bacterial, implying that these are products of one or more lateral gene transfer events post-dating the cnidarian-bilaterian divergence. The deployment by corals of genes used by bacteria to compete with other bacteria reflects a mechanism of microbiome manipulation previously unknown in Metazoa but that may apply more generally.

Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria

Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.

Skimming genomes for systematics and DNA barcodes of corals

Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia

Bioluminescence is a widespread phenomenon that has evolved multiple times across the tree of life, converging among diverse fauna and habitat types. The ubiquity of bioluminescence, particularly in marine environments where it is commonly used for communication and defense, highlights the adaptive value of this trait, though the evolutionary origins and timing of emergence remain elusive for a majority of luminous organisms. Anthozoan cnidarians are a diverse group of animals with numerous bioluminescent species found throughout the world's oceans, from shallow waters to the light-limited deep sea where bioluminescence is particularly prominent. This study documents the presence of bioluminescent Anthozoa across depth and explores the diversity and evolutionary origins of bioluminescence among Octocorallia-a major anthozoan group of marine luminous organisms. Using a phylogenomic approach and ancestral state reconstruction, we provide evidence for a single origin of bioluminescence in Octocorallia and infer the age of occurrence to around the Cambrian era, approximately 540 Ma-setting a new record for the earliest timing of emergence of bioluminescence in the marine environment. Our results further suggest this trait was largely maintained in descendants of a deep-water ancestor and bioluminescent capabilities may have facilitated anthozoan diversification in the deep sea.

Unravelling the relationships among Madrepora Linnaeus, 1758, Oculina Lamark, 1816 and Cladocora Ehrenberg, 1834 (Cnidaria: Anthozoa: Scleractinia)

Despite the widespread use of integrative taxonomic approaches, many scleractinian coral genera and species remain grouped in polyphyletic families, classified as incertae sedis or simply understudied. Oculinidae Gray, 1847 represents a family for which many taxonomic questions remain unresolved, particularly those related to some of the current genera, such as Oculina Lamark, 1816 or recently removed genera, including Cladocora Ehrenberg, 1834 and Madrepora Linnaeus, 1758. Cladocora is currently assigned to the family Cladocoridae Milne Edwards & Haime, 1857 and a new family, Bathyporidae Kitahara, Capel, Zilberberg & Cairns, 2024, was recently raised to accommodate Madrepora . However, the name Bathyporidae is not valid because this was not formed on the basis of a type genus name. To resolve taxonomic questions related to these three genera, the evolutionary relationships are explored through phylogenetic analyses of 18 molecular markers. The results of these analyses support a close relationship between the species Oculina patagonica and Cladocora caespitosa , indicating that these may belong to the same family (and possibly genus), and highlighting the need for detailed revisions of Oculina and Cladocora . By contrast, a distant relationship is found between these two species and Madrepora oculata , with the overall evidence supporting the placement of Madrepora in the resurrected family Madreporidae Ehrenberg, 1834. This study advances our knowledge of coral systematics and highlights the need for a comprehensive review of the genera Oculina , Cladocora and Madrepora .

Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)

Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.

300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia)

The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.

Evolutionary Analysis of Cnidaria Small Cysteine-Rich Proteins (SCRiPs), an Enigmatic Neurotoxin Family from Stony Corals and Sea Anemones (Anthozoa: Hexacorallia)

Cnidarians (corals, sea anemones, and jellyfish) produce toxins that play central roles in key ecological processes, including predation, defense, and competition, being the oldest extant venomous animal lineage. Cnidaria small cysteine-rich proteins (SCRiPs) were the first family of neurotoxins detected in stony corals, one of the ocean's most crucial foundation species. Yet, their molecular evolution remains poorly understood. Moreover, the lack of a clear classification system has hindered the establishment of an accurate and phylogenetically informed nomenclature. In this study, we extensively surveyed 117 genomes and 103 transcriptomes of cnidarians to identify orthologous SCRiP gene sequences. We annotated a total of 168 novel putative SCRiPs from over 36 species of stony corals and 12 species of sea anemones. Phylogenetic reconstruction identified four distinct SCRiP subfamilies, according to strict discrimination criteria based on well-supported monophyly with a high percentage of nucleotide and amino acids' identity. Although there is a high prevalence of purifying selection for most SCRiP subfamilies, with few positively selected sites detected, a subset of Acroporidae sequences is influenced by diversifying positive selection, suggesting potential neofunctionalizations related to the fine-tuning of toxin potency. We propose a new nomenclature classification system relying on the phylogenetic distribution and evolution of SCRiPs across Anthozoa, which will further assist future proteomic and functional research efforts.

How long have we been mistaken? Multi-tools shedding light into the systematics of the widespread deep-water genus Madrepora Linnaeus, 1758 (Scleractinia)

Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora, which contains M. oculata, one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora, while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora, resolve a long-standing question regarding the phylogenetic position of the genus, and highlight the need of a worldwide review of the genus.

Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum

The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.

Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata

Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with our ability to control spawning in the laboratory, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research.

Bamboozled! Resolving deep evolutionary nodes within the phylogeny of bamboo corals (Octocorallia: Scleralcyonacea: Keratoisididae)

Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups - D1 and D2, and A1 and M1 - needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters.

Genetic adaptations of sea anemone to hydrothermal environment

Hydrothermal vent habitats are characterized by high hydrostatic pressure, darkness, and the continuous release of toxic metal ions into the surrounding environment where sea anemones and other invertebrates thrive. Nevertheless, the understanding of metazoan metal ion tolerances and environmental adaptations remains limited. We assembled a chromosome-level genome for the vent sea anemone, Alvinactis idsseensis sp. nov. Comparative genomic analyses revealed gene family expansions and gene innovations in A. idsseensis sp. nov. as a response to high concentrations of metal ions. Impressively, the metal tolerance proteins MTPs is a unique evolutionary response to the high concentrations of Fe2+ and Mn2+ present in the environments of these anemones. We also found genes associated with high concentrations of polyunsaturated fatty acids that may respond to high hydrostatic pressure and found sensory and circadian rhythm-regulated genes that were essential for adaptations to darkness. Overall, our results provide insights into metazoan adaptation to metal ions, high pressure, and darkness in hydrothermal vents.

Bellactis lux n. sp. (Cnidaria: Anthozoa: Actiniaria: Aiptasiidae), a new sea anemone from the Gulf of Mexico

Here we describe a new species of sea anemone from the family Aiptasiidae based on specimens collected from the Gulf of Mexico (USA: Florida & Alabama). Accounts of this species have been known since the early 1990s, primarily from an underwater field guide and hobbyist aquarium literature under the name Lightbulb Anemone. We describe it as a new species from the genus Bellactis based on anatomy, histology, and cnidom. Members of this species are small in size, with a smooth, typically contracted column divided into regions based on color and bearing rows of two or three elevated cinclides in the mid column. Their tentacles are distinctive, translucent, distally inflated and can be bulbous in shape, with sub annular rings. This description synthesizes information about Bellactis and contextualizes what is known about its diversity in light of other members of the Aiptasiidae.

Bathymetric evolution of black corals through deep time

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

A predatory gastrula leads to symbiosis-independent settlement in Aiptasia

The planula larvae of the sea anemone Aiptasia have so far not been reported to complete their life cycle by undergoing metamorphosis into adult forms. This has been a major obstacle in their use as a model for coral-dinoflagellate endosymbiosis. Here, we show that Aiptasia larvae actively feed on crustacean nauplii, displaying a preference for live prey. This feeding behavior relies on functional stinging cells, indicative of complex neuronal control. Regular feeding leads to significant size increase, morphological changes, and efficient settlement around 14 d postfertilization. Surprisingly, the presence of dinoflagellate endosymbionts does not affect larval growth or settlement dynamics but is crucial for sexual reproduction. Our findings finally close Aiptasia's life cycle and highlight the functional nature of its larvae, as in Haeckel's Gastrea postulate, yet reveal its active carnivory, thus contributing to our understanding of early metazoan evolution.

Potential of MALDI-TOF MS-based proteomic fingerprinting for species identification of Cnidaria across classes, species, regions and developmental stages

Morphological identification of cnidarian species can be difficult throughout all life stages due to the lack of distinct morphological characters. Moreover, in some cnidarian taxa genetic markers are not fully informative, and in these cases combinations of different markers or additional morphological verifications may be required. Proteomic fingerprinting based on MALDI-TOF mass spectra was previously shown to provide reliable species identification in different metazoans including some cnidarian taxa. For the first time, we tested the method across four cnidarian classes (Staurozoa, Scyphozoa, Anthozoa, Hydrozoa) and included different scyphozoan life-history stages (polyp, ephyra, medusa) in our dataset. Our results revealed reliable species identification based on MALDI-TOF mass spectra across all taxa with species-specific clusters for all 23 analysed species. In addition, proteomic fingerprinting was successful for distinguishing developmental stages, still by retaining a species specific signal. Furthermore, we identified the impact of different salinities in different regions (North Sea and Baltic Sea) on proteomic fingerprints to be negligible. In conclusion, the effects of environmental factors and developmental stages on proteomic fingerprints seem to be low in cnidarians. This would allow using reference libraries built up entirely of adult or cultured cnidarian specimens for the identification of their juvenile stages or specimens from different geographic regions in future biodiversity assessment studies.

Cerianthus lloydii (Ceriantharia: Anthozoa: Cnidaria): New Status and New Perspectives

Subclass Ceriantharia is a well-defined and probably ancient group of marine benthic organisms renowned for their bilateral symmetry, which is reflected in the arrangement of tentacles and mesenteries. Four species of Ceriantharia have been reported in the Arctic, including Cerianthus lloydii Gosse, 1859, also known from the Northern Atlantic and Northern Pacific. The integrity of this species was questioned in the literature, so we performed a molecular study of C. lloydii from several geographically distant locations using 18S and COI genes. The phylogenetic reconstructions show that specimens of C. lloydii form a single group with high support (>0.98), subdivided into distinctive clades: (1) specimens from Northern Europe, the Black and Barents seas, and (2) specimens from the White, Kara, Laptev, and Bering seas and also the Canadian Arctic and the Labrador Sea available via the BOLD database. There are several BOLD COI sequences of Pachycerianthus borealis (Verrill, 1873), which form a third clade of the C. lloydii group, sister to the European and Arctic clades. Based on low similarity (COI 86-87%) between C. lloydii and the type species of the genus Cerianthus Delle Chiaje, 1841-C. membranaceus (Gmelin, 1791), we propose a new status for the genus Synarachnactis Carlgren, 1924, and a new family Synarachnactidae to accommodate C. lloydii.

A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.

Genomic, functional and structural analyses elucidate evolutionary innovation within the sea anemone 8 toxin family

BACKGROUND

The ShK toxin from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in Actiniarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni, characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T. stephensoni.

RESULTS

We identified ten SA8-family genes in two clusters and six SA8-family genes in five clusters for T. stephensoni and A. tenebrosa, respectively. Nine SA8 T. stephensoni genes were found in a single cluster, and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While the functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity.

CONCLUSIONS

Our results provide the first demonstration that SA8 is a unique gene family in Actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T. stephensoni.

Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution.

Selection in coral mitogenomes, with insights into adaptations in the deep sea

Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean's surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject to selection pressures at greater depths to meet the metabolic demands of that environment. Here, we use a phylogenomic framework combined with codon-based models to evaluate whether mt protein-coding genes (PCGs) associated with cellular energy functions are under positive selection across depth in three groups of corals: Octocorallia, Scleractinia, and Antipatharia. The results demonstrated that mt PCGs of deep- and shallow-water species of all three groups were primarily under strong purifying selection (0.0474 < ω < 0.3123), with the exception of positive selection in atp6 (ω = 1.3263) of deep-sea antipatharians. We also found evidence for positive selection at fifteen sites across cox1, mtMutS, and nad1 in deep-sea octocorals and nad3 of deep-sea antipatharians. These results contribute to our limited understanding of mt adaptations as a function of depth and provide insight into the molecular response of corals to the extreme deep-sea environment.

Genome assembly of the deep-sea coral Lophelia pertusa

Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.

First In Situ Observation of Sperm Release in Corynactis carnea (Anthozoa: Corallimorpharia) from Patagonia, Argentina

Jewel sea anemones constitute a relatively small group of solitary cnidarians, a sister group of scleractinian corals. In the southwest Atlantic Ocean off Argentina, two species of jewel sea anemones have been found: Corynactis carnea and Corallimorphus rigidus. Corynactis carnea is a common and abundant species in shallow water of northern Atlantic Patagonia, but reproductive data on this species is scarce; the species is known to reproduce asexually. During a SCUBA diving survey in an Atlantic rocky reefs (20 m depth) in Patagonia, we observed for the first time specimens of C. carnea releasing sperm, eight days after the full moon and during the summer season while spawning has been previously observed in at least three species of Corynactis, but all were recorded as occurring in winter.

Single-cell atavism reveals an ancient mechanism of cell type diversification in a sea anemone

Cnidocytes are the explosive stinging cells unique to cnidarians (corals, jellyfish, etc). Specialized for prey capture and defense, cnidocytes comprise a group of over 30 morphologically and functionally distinct cell types. These unusual cells are iconic examples of biological novelty but the developmental mechanisms driving diversity of the stinging apparatus are poorly characterized, making it challenging to understand the evolutionary history of stinging cells. Using CRISPR/Cas9-mediated genome editing in the sea anemone Nematostella vectensis, we show that a single transcription factor (NvSox2) acts as a binary switch between two alternative stinging cell fates. Knockout of NvSox2 causes a transformation of piercing cells into ensnaring cells, which are common in other species of sea anemone but appear to have been silenced in N. vectensis. These results reveal an unusual case of single-cell atavism and expand our understanding of the diversification of cell type identity.

There and Back Again: The Unexpected Journeys of Metridium de Blainville, 1824 between the Old Oceans and throughout the Modern World

AbstractMembers of the sea anemone genus Metridium are abundant in temperate rocky habitats and fouling communities. Their biogeographic history is expected to reflect changes in currents and habitats that have influenced benthic communities, such as the climate-influenced changes that occurred during the Last Glacial Maximum. More recently, however, anthropogenic influences such as shipping transportation and the creation of artificial habitat have altered and affected the composition of modern-day marine communities. Here we use sequence-capture data to examine the genetic structure of Metridium across its shallow-water distribution to (1) evaluate species boundaries within Metridium, (2) elucidate the dispersal history of Metridium between and among oceans, and (3) assess the influence of anthropogenic movement on modern-day populations. We find strong evidence for two species within Metridium: M. farcimen and M. senile. Dispersal from the Pacific to the Atlantic included a subsequent isolation of a small population in or above the Bering Sea, which has presumably moved southward. Within the native range of M. senile, admixture is prevalent even between oceans as a result of anthropogenic activities. The nonnative populations in Chile and the Falkland Islands came from at least two distinct introduction events originating from both coasts of the United States in the North Pacific and North Atlantic Oceans. Hybridization between M. senile and M. farcimen is documented as occurring in anthropogenically influenced habitats. The heavy influence from anthropogenic activities will continue to impact our understanding of marine organisms, particularly within the native range and for those that are easily transported across long distances.

Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes

In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.

Micro and macroevolution of sea anemone venom phenotype

Venom is a complex trait with substantial inter- and intraspecific variability resulting from strong selective pressures acting on the expression of many toxic proteins. However, understanding the processes underlying toxin expression dynamics that determine the venom phenotype remains unresolved. By interspecific comparisons we reveal that toxin expression in sea anemones evolves rapidly and that in each species different toxin family dictates the venom phenotype by massive gene duplication events. In-depth analysis of the sea anemone, Nematostella vectensis, revealed striking variation of the dominant toxin (Nv1) diploid copy number across populations (1-24 copies) resulting from independent expansion/contraction events, which generate distinct haplotypes. Nv1 copy number correlates with expression at both the transcript and protein levels with one population having a near-complete loss of Nv1 production. Finally, we establish the dominant toxin hypothesis which incorporates observations in other venomous lineages that animals have convergently evolved a similar strategy in shaping their venom.

Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement

Hox and ParaHox transcription factors are important for specifying cell fates along the primary body axes during the development of most animals. Within Cnidaria, much of the research on Hox/ParaHox genes has focused on Anthozoa (anemones and corals) and Hydrozoa (hydroids) and has concentrated on the evolution and function of cnidarian Hox genes in relation to their bilaterian counterparts. Here we analyze together the full complement of Hox and ParaHox genes from species representing all four medusozoan classes (Staurozoa, Cubozoa, Hydrozoa, and Scyphozoa) and both anthozoan classes (Octocorallia and Hexacorallia). Our results show that Hox genes involved in patterning the directive axes of anthozoan polyps are absent in the stem leading to Medusozoa. For the first time, we show spatial and temporal expression patterns of Hox and ParaHox genes in the upside-down jellyfish Cassiopea xamachana (Scyphozoa), which are consistent with diversification of medusozoan Hox genes both from anthozoans and within medusozoa. Despite unprecedented taxon sampling, our phylogenetic analyses, like previous studies, are characterized by a lack of clear homology between most cnidarian and bilaterian Hox and Hox-related genes. Unlike previous studies, we propose the hypothesis that the cnidarian-bilaterian ancestor possessed a remarkably large Hox complement and that extensive loss of Hox genes was experienced by both cnidarian and bilaterian lineages.

Ediacaran Corumbella has a cataphract calcareous skeleton with controlled biomineralization

Corumbella is a terminal Ediacaran tubular, benthic fossil of debated morphology, composition, and biological affinity. Here, we show that Corumbella had a biomineralized skeleton, with a bilayered construction of imbricated calcareous plates and rings (sclerites) yielding a cataphract organization, that enhanced flexibility. Each sclerite likely possessed a laminar microfabric with consistent crystallographic orientation, within an organic matrix. Original aragonitic mineralogy is supported by relict aragonite and elevated Sr (mean = ca. 11,800 ppm in central parts of sclerites). In sum, the presence of a polarisation axis, sclerites with a laminar microfabric, and a cataphract skeletal organization reminiscent of early Cambrian taxa, are all consistent with, but not necessarily indicative of, a bilaterian affinity. A cataphract skeleton with an inferred complex microstructure confirms the presence of controlled biomineralization in metazoans by the terminal Ediacaran, and offers insights into the evolution of development and ecology at the root of the 'Cambrian radiation'.