A simple plan — cnidarians and the origins of developmental mechanisms

Embryonic Development of the Gastrodermis in the Coral Acropora tenuis

Due to limited spawning seasons, embryogenesis of corals has not fully been studied and the embryonic origin of gastrodermis remains uncertain in Acropora. We herein examined how embryonic endodermal cells develop into the gastrodermis and mesentery of polyps in Acropora tenuis. In juvenile polyps, the gastrodermis invaginates to form mesenteries, both of which were stained with rhodamine-phalloidin, an anti-myocyte-specific enhancer factor 2 (anti-AtMef2) antibody, and an anti-lipoxygenase homology domain-containing protein 1 (anti-AtLoxhd1) antibody. Rhoda-mine-phalloidin staining was traced back to the endodermal cells of 60-85 hpf 'pear'-stage embryos through the larval stage. AtMef2 appeared in the blastomeres of a 12-hpf 'prawnchip'-stage embryo that was a variant U-shaped blastula with a narrow blastocoel. AtMef2 temporarily disappeared from the nuclei of 28-hpf 'donut'-stage embryos and reappeared in the endodermal cells of 40-hpf early 'pear'-stage embryos, suggesting a transition from maternal to zygotic expression of Mef2. The blastopore closed without the invagination of blastomeres. The gastrocoel collapsed and the Mef2-positive endoderm was dissociated into single cells in the well-developed blastocoel filled with yolk cells. The mesoglea appeared in the yolk cell layer. AtLoxhd1 was traced back to the endodermal cells of 'pear'-stage embryos. In 11-dpf larvae, Loxhd1-positive endodermal cells elongated in the vicinity of the mesoglea to adhere to each other and form the gastroderm epithelium in larvae. Therefore, in this coral, the inner wall of U-shaped early embryos is the cellular origin of the gastrodermis. Inner wall-derived endodermal cells move independently toward the mesoglea, where cell-cell adhesion occurs to establish the gastrodermis.

'Three signals - three body axes' as patterning principle in bilaterians

In vertebrates, the three orthogonal body axes, anteroposterior (AP), dorsoventral (DV) and left-right (LR) are determined at gastrula and neurula stages by the Spemann-Mangold organizer and its equivalents. A common feature of AP and DV axis formation is that an evolutionary conserved interplay between growth factors (Wnt, BMP) and their extracellular antagonists (e.g. Dkk1, Chordin) creates signaling gradients for axial patterning. Recent work showed that LR patterning in Xenopus follows the same principle, with R-spondin 2 (Rspo2) as an extracellular FGF antagonist, which creates a signaling gradient that determines the LR vector. That a triad of anti-FGF, anti-BMP, and anti-Wnt governs LR, DV, and AP axis formation reveals a unifying principle in animal development. We discuss how cross-talk between these three signals confers integrated AP-DV-LR body axis patterning underlying developmental robustness, size scaling, and harmonious regulation. We propose that Urbilateria featured three orthogonal body axes that were governed by a Cartesian coordinate system of orthogonal Wnt/AP, BMP/DV, and FGF/LR signaling gradients.

First insights into the Aurelia aurita transcriptome response upon manipulation of its microbiome

Introduction

The associated diverse microbiome contributes to the overall fitness of Aurelia aurita, particularly to asexual reproduction. However, how A. aurita maintains this specific microbiome or reacts to manipulations is unknown.

Methods

In this report, the response of A. aurita to manipulations of its native microbiome was studied by a transcriptomics approach. Microbiome-manipulated polyps were generated by antibiotic treatment and challenging polyps with a non-native, native, and potentially pathogenic bacterium. Total RNA extraction followed by RNAseq resulted in over 155 million reads used for a de novo assembly.

Results

The transcriptome analysis showed that the antibiotic-induced change and resulting reduction of the microbiome significantly affected the host transcriptome, e.g., genes involved in processes related to immune response and defense mechanisms were highly upregulated. Similarly, manipulating the microbiome by challenging the polyp with a high load of bacteria (2 × 107 cells/polyp) resulted in induced transcription of apoptosis-, defense-, and immune response genes. A second focus was on host-derived quorum sensing interference as a potential defense strategy. Quorum Quenching (QQ) activities and the respective encoding QQ-ORFs of A. aurita were identified by functional screening a cDNA-based expression library generated in Escherichia coli. Corresponding sequences were identified in the transcriptome assembly. Moreover, gene expression analysis revealed differential expression of QQ genes depending on the treatment, strongly suggesting QQ as an additional defense strategy.

Discussion

Overall, this study allows first insights into A. aurita's response to manipulating its microbiome, thus paving the way for an in-depth analysis of the basal immune system and additional fundamental defense strategies.

The Repertoire of Tissue Inhibitors of Metalloproteases: Evolution, Regulation of Extracellular Matrix Proteolysis, Engineering and Therapeutic Challenges

Tissue inhibitors of metalloproteases (TIMPs) belong to a fascinating protein family expressed in all Metazoa. They act as regulators of the turnover of the extracellular matrix, and they are consistently involved in essential processes. Herein, we recapitulate the main activities of mammalian TIMPs (TIMP1-4) in the control of extracellular-matrix degradation and pathologies associated with aberrant proteostasis. We delineate the activity of TIMPs in the control of extracellular matrix (ECM) homeostasis and discuss the diversity of TIMPs across metazoans taking into account the emergence of the components of the ECM during evolution. Thus, the TIMP repertoire herein analysed includes the homologues from cnidarians, which are coeval with the origins of ECM components; protostomes (molluscs, arthropods and nematodes); and deuterostomes (echinoderms and vertebrates). Several questions, including the maintenance of the structure despite low sequence similarity and the strategies for TIMP engineering, shed light on the possibility to use recombinant TIMPs integrating unique features and binding selectivity for therapeutic applications in the treatment of inflammatory pathologies.

Hypoxia as a physiological cue and pathological stress for coral larvae

Ocean deoxygenation events are intensifying worldwide and can rapidly drive adult corals into a state of metabolic crisis and bleaching-induced mortality, but whether coral larvae are subject to similar stress remains untested. We experimentally exposed apo-symbiotic coral larvae of Acropora selago to deoxygenation stress with subsequent reoxygenation aligned to their night-day light cycle, and followed their gene expression using RNA-Seq. After 12 h of deoxygenation stress (~2 mg O₂ /L), coral planulae demonstrated a low expression of HIF-targeted hypoxia response genes concomitant with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult corals. Despite exhibiting a consistent swimming phenotype compared to control samples, the differential gene expression observed in planulae exposed to deoxygenation-reoxygenation suggests a disruption of pathways involved in developmental regulation, mitochondrial activity, lipid metabolism, and O₂ -sensitive epigenetic regulators. Importantly, we found that treated larvae exhibited a disruption in the expression of conserved HIF-targeted developmental regulators, for example, Homeobox (HOX) genes, corroborating how changes in external oxygen levels can affect animal development. We discuss how the observed deoxygenation responses may be indicative of a possible acclimation response or alternatively may imply negative latent impacts for coral larval fitness.

Studying evolution of the primary body axis in vivo and in vitro

The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model organisms, underlying principles of many early patterning processes nevertheless remain enigmatic. Despite the diversity of (pre-)gastrulating embryo and adult body shapes across the animal kingdom, the body axes, which are arguably the most fundamental features, generally remain identical between phyla. Recently there has been a renewed appreciation of ex vivo and in vitro embryo-like systems to model early embryonic patterning events. Here, we briefly review key examples and propose that similarities in morphogenesis and associated gene expression dynamics may reveal an evolutionarily conserved developmental mode as well as provide further insights into the role of external or extraembryonic cues in shaping the early embryo. In summary, we argue that embryo-like systems can be employed to inform previously uncharted aspects of animal body plan evolution as well as associated patterning rules.

Cellular pathways during spawning induction in the starlet sea anemone Nematostella vectensis

In cnidarians, long-term ecological success relies on sexual reproduction. The sea anemone Nematostella vectensis, which has emerged as an important model organism for developmental studies, can be induced for spawning by temperature elevation and light exposure. To uncover molecular mechanisms and pathways underlying spawning, we characterized the transcriptome of Nematostella females before and during spawning induction. We identified an array of processes involving numerous receptors, circadian clock components, cytoskeleton, and extracellular transcripts that are upregulated upon spawning induction. Concurrently, processes related to the cell cycle, fatty acid metabolism, and other housekeeping functions are downregulated. Real-time qPCR revealed that light exposure has a minor effect on expression levels of most examined transcripts, implying that temperature change is a stronger inducer for spawning in Nematostella. Our findings reveal the potential mechanisms that may enable the mesenteries to serve as a gonad-like tissue for the developing oocytes and expand our understanding of sexual reproduction in cnidarians.

Gastrulation and germ layer formation in the sea anemone Nematostella vectensis and other cnidarians

Among the basally branching metazoans, cnidarians display well-defined gastrulation processes leading to a diploblastic body plan, consisting of an endodermal and an ectodermal cell layer. As the outgroup to all Bilateria, cnidarians are an interesting group to investigate ancestral developmental mechanisms. Interestingly, all known gastrulation mechanisms known in Bilateria are already found in different species of Cnidaria. Here I review the morphogenetic processes found in different Cnidaria and focus on the investigation of the cellular and molecular mechanisms in the sea anemone Nematostella vectensis, which has been a major model organism among cnidarians for evolutionary developmental biology. Many of the genes involved in germ layer specification and morphogenetic processes in Bilateria are also found active during gastrulation of Nematostella and other cnidarians, suggesting an ancestral role of this process. The molecular analyses indicate a tight link between gastrulation and axis patterning processes by Wnt and FGF signaling. Interestingly, the endodermal layer displays many features of the mesodermal layer in Bilateria, while the pharyngeal ectoderm has an endodermal expression profile. Comparative analyses as well as experimental studies using embryonic aggregates suggest that minor differences in the gene regulatory networks allow the embryo to transition relatively easily from one mode of gastrulation to another.

Hydra vulgaris exhibits day-night variation in behavior and gene expression levels

BACKGROUND

Day-night behavioral variation is observed in most organisms, and is generally controlled by circadian clocks and/or synchronization to environmental cues. Hydra species, which are freshwater cnidarians, are thought to lack the core clock genes that form transcription-translation feedback loops in clock systems. In this study, we examined whether hydras exhibit diel rhythms in terms of behavior and gene expression levels without typical clock genes.

RESULTS

We found that the total behavior of hydras was elevated during the day and decreased at night under a 12-h light-dark cycle. Polyp contraction frequency, one component of behavior, exhibited a clear diel rhythm. However, neither total behavior nor polyp contraction frequency showed rhythmic changes under constant light and constant dark conditions. To identify the genes underlying diel behavior, we performed genome-wide transcriptome analysis of hydras under light-dark cycles. Using three different analytic algorithms, we found that 380 genes showed robust diel oscillations in expression. Some of these genes shared common features with diel cycle genes of other cnidarian species with endogenous clock systems.

CONCLUSION

Hydras show diel behavioral rhythms under light-dark cycles despite the absence of canonical core clock genes. Given the functions of the genes showing diel oscillations in hydras and the similarities of those genes with the diel cycle genes of other cnidarian species with circadian clocks, it is possible that diel cycle genes play an important role across cnidarian species regardless of the presence or absence of core clock genes under light-dark cycles.

Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral

Can genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomics, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coral Acropora millepora on the Great Barrier Reef (GBR). Genomics-derived migration rates were high (0.1–1% of immigrants per generation across half the latitudinal range of the GBR) and closely matched the biophysical model of larval dispersal. Both genetic and biophysical models indicated the prevalence of southward migration along the GBR that would facilitate the spread of heat-tolerant alleles to higher latitudes as the climate warms. We developed an individual-based metapopulation model of polygenic adaptation and parameterized it with population sizes and migration rates derived from the genomic analysis. We find that high migration rates do not disrupt local thermal adaptation, and that the resulting standing genetic variation should be sufficient to fuel rapid region-wide adaptation of A. millepora populations to gradual warming over the next 20–50 coral generations (100–250 years). Further adaptation based on novel mutations might also be possible, but this depends on the currently unknown genetic parameters underlying coral thermal tolerance and the rate of warming realized. Despite this capacity for adaptation, our model predicts that coral populations would become increasingly sensitive to random thermal fluctuations such as ENSO cycles or heat waves, which corresponds well with the recent increase in frequency of catastrophic coral bleaching events.

Coral reefs worldwide are suffering high mortality from severe thermal stress episodes induced by acute ocean warming events. Under the current rate of warming, will corals be gone before the end of this century? Here we combine population genomics with biophysical and evolutionary modeling to investigate adaptive potential of a common reef-building coral from the Great Barrier Reef. To approach this task, we have developed a predictive model of polygenic adaptation in a system of multiple inter-connected populations that exist in a heterogeneous and changing environment. Applying this model to our coral species, we find that populations successfully adapt to diverse local temperatures along the range of the Great Barrier Reef despite high migrant exchange and should collectively harbor enough adaptive genetic variants to fuel region-wide thermal adaptation for another century and perhaps longer. In the same time, the model predicts that random thermal fluctuations will induce increasingly severe coral mortality episodes, which aligns well with observations over the last few decades.

Characterization of Translationally Controlled Tumour Protein from the Sea Anemone Anemonia viridis and Transcriptome Wide Identification of Cnidarian Homologues

Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure. The pattern of mRNA expression profile was also defined in A. viridis. These analyses revealed a constitutive mRNA expression especially in tissues with active proliferation. Additionally, the transcriptional profile of A. viridis TCTP (AvTCTP) after challenges with different abiotic/biotic stresses showed induction by extreme temperatures, heavy metals exposure and immune stimulation. These results suggest the involvement of AvTCTP in the sea anemone defensome taking part in environmental stress and immune responses.

Evolutionary conserved mechanisms pervade structure and transcriptional modulation of allograft inflammatory factor-1 from sea anemone Anemonia viridis

Gene family encoding allograft inflammatory factor-1 (AIF-1) is well conserved among organisms; however, there is limited knowledge in lower organisms. In this study, the first AIF-1 homologue from cnidarians was identified and characterised in the sea anemone Anemonia viridis. The full-length cDNA of AvAIF-1 was of 913 bp with a 5' -untranslated region (UTR) of 148 bp, a 3'-UTR of 315 and an open reading frame (ORF) of 450 bp encoding a polypeptide with149 amino acid residues and predicted molecular weight of about 17 kDa. The predicted protein possesses evolutionary conserved EF hand Ca²⁺ binding motifs, post-transcriptional modification sites and a 3D structure which can be superimposed with human members of AIF-1 family. The AvAIF-1 transcript was constitutively expressed in all tested tissues of unchallenged sea anemone, suggesting that AvAIF-1 could serve as a general protective factor under normal physiological conditions. Moreover, we profiled the transcriptional activation of AvAIF-1 after challenges with different abiotic/biotic stresses showing induction by warming conditions, heavy metals exposure and immune stimulation. Thus, mechanisms associated to inflammation and immune challenges up-regulated AvAIF-1 mRNA levels. Our results suggest its involvement in the inflammatory processes and immune response of A. viridis.

The Mesoderm-Forming Gene brachyury Regulates Ectoderm-Endoderm Demarcation in the Coral Acropora digitifera

Blastoporal expression of the T-box transcription factor gene brachyury is conserved in most metazoans [1, 2]. Its role in mesoderm formation has been intensively studied in vertebrates [3-6]. However, its fundamental function near the blastopore is poorly understood in other phyla. Cnidarians are basal metazoans that are important for understanding evolution of metazoan body plans [7, 8]. Because they lack mesoderm, they have been used to investigate the evolutionary origins of mesoderm [1, 9-11]. Here, we focus on corals, a primitive clade of cnidarians that diverged from sea anemones ∼500 mya [12]. We developed a microinjection method for coral eggs to examine Brachyury functions during embryogenesis of the scleractinian coral, Acropora digitifera. Because Acropora embryos undergo pharynx formation after the blastopore closes completely [13-15], they are useful to understand Brachyury functions in gastrulation movement and pharynx formation. We show that blastoporal expression of brachyury is directly activated by Wnt/β-catenin signaling in the ectoderm of coral embryos, indicating that the regulatory axis from Wnt/β-catenin signaling to brachyury is highly conserved among eumetazoans. Loss-of-function analysis demonstrated that Brachyury is required for pharynx formation but not for gastrulation movement. Genome-wide transcriptome analysis demonstrated that genes positively regulated by Brachyury are expressed in the ectoderm of Acropora gastrulae, while negatively regulated genes are in endoderm. Therefore, germ layer demarcation around the blastopore appears to be the evolutionarily conserved role of Brachyury during gastrulation. Compared with Brachyury functions in vertebrate mesoderm-ectoderm and mesoderm-endoderm demarcation [4-6], our results suggest that the vertebrate-type mesoderm may have originated from brachyury-expressing ectoderm adjacent to endoderm.

Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years

Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations.

A new paradigm for animal symmetry

My aim in this article is to soften certain rigid concepts concerning the radial and bilateral symmetry of the animal body plan, and to offer a more flexible framework of thinking for them, based on recent understandings of how morphogenesis is regulated by the mosaically acting gene regulatory networks. Based on general principles of the genetic regulation of morphogenesis, it can be seen that the difference between the symmetry of the whole body and that of minor anatomical structures is only a question of a diverse timing during development. I propose that the animal genome, as such, is capable of expressing both radial and bilateral symmetries, and deploys them according to the functional requirements which must be satisfied by both the anatomical structure and body as a whole. Although it may seem paradoxical, this flexible view of symmetry, together with the idea that symmetry is strongly determined by function, bolsters the concept that the presence of the two main symmetries in the animal world is not due to chance: they are necessary biological patterns emerging in evolution.

A deuterostome origin of the Spemann organiser suggested by Nodal and ADMPs functions in Echinoderms

During development of chordates, establishment of the body plan relies on the activity of an organizing centre located on the dorsal side of the embryo that patterns the embryo and induces neural tissue. Intriguingly, the evolutionary origin of this crucial signalling centre remains unclear and whether analogous organizers regulate D/V patterning in other deuterostome or protostome phyla is not known. Here we provide evidence that the ventral ectoderm of the sea urchin embryo is a long-range organizing centre that shares several fundamental properties with the Spemann organizer: the ability to induce duplicated embryonic axes when ectopically induced, the ability to induce neural fate in neighbouring tissues and the ability to finely regulate the level of BMP signalling by using an autoregulatory expansion–repression mechanism. These findings suggest that the evolutionary origin of the Spemann organizer is more ancient than previously thought and that it may possibly be traced back to the common ancestor of deuterostomes.

Establishment of the body plan in chordates is determined by an organizing centre located on the dorsal side of the embryo. Here, the authors show that the ventral ectoderm of the sea urchin embryo is an organizing centre that shares several fundamental properties with the amphibian Spemann organizer.

Profiling molecular and behavioral circadian rhythms in the non-symbiotic sea anemone Nematostella vectensis

Endogenous circadian clocks are poorly understood within early-diverging animal lineages. We have characterized circadian behavioral patterns and identified potential components of the circadian clock in the starlet sea anemone, Nematostella vectensis: a model cnidarian which lacks algal symbionts. Using automatic video tracking we showed that Nematostella exhibits rhythmic circadian locomotor activity, which is persistent in constant dark, shifted or disrupted by external dark/light cues and maintained the same rate at two different temperatures. This activity was inhibited by a casein kinase 1δ/ε inhibitor, suggesting a role for CK1 homologue(s) in Nematostella clock. Using high-throughput sequencing we profiled Nematostella transcriptomes over 48 hours under a light-dark cycle. We identified 180 Nematostella diurnally-oscillated transcripts and compared them with previously established databases of adult and larvae of the symbiotic coral Acropora millepora, revealing both shared homologues and unique rhythmic genes. Taken together, this study further establishes Nematostella as a non-symbiotic model organism to study circadian rhythms and increases our understanding about the fundamental elements of circadian regulation and their evolution within the Metazoa

The genetics of colony form and function in Caribbean Acropora corals

Background

Colonial reef-building corals have evolved a broad spectrum of colony morphologies based on coordinated asexual reproduction of polyps on a secreted calcium carbonate skeleton. Though cnidarians have been shown to possess and use similar developmental genes to bilaterians during larval development and polyp formation, little is known about genetic regulation of colony morphology in hard corals. We used RNA-seq to evaluate transcriptomic differences between functionally distinct regions of the coral (apical branch tips and branch bases) in two species of Caribbean Acropora, the staghorn coral, A. cervicornis, and the elkhorn coral, A. palmata.

Results

Transcriptome-wide gene profiles differed significantly between different parts of the coral colony as well as between species. Genes showing differential expression between branch tips and bases were involved in developmental signaling pathways, such as Wnt, Notch, and BMP, as well as pH regulation, ion transport, extracellular matrix production and other processes. Differences both within colonies and between species identify a relatively small number of genes that may contribute to the distinct “staghorn” versus “elkhorn” morphologies of these two sister species.

Conclusions

The large number of differentially expressed genes supports a strong division of labor between coral branch tips and branch bases. Genes involved in growth of mature Acropora colonies include the classical signaling pathways associated with development of cnidarian larvae and polyps as well as morphological determination in higher metazoans.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1133) contains supplementary material, which is available to authorized users.

Predation and the origin of neurones

The core design of spiking neurones is remarkably similar throughout the animal kingdom. Their basic function as fast-signalling thresholding cells might have been established very early in their evolutionary history. Identifying the selection pressures that drove animals to evolve spiking neurones could help us interpret their design and function today. We review fossil, ecological and molecular evidence to investigate when and why animals evolved spiking neurones. Fossils suggest that animals evolved nervous systems soon after the advent of animal-on-animal predation, 550 million years ago (MYa). Between 550 and 525 MYa, we see the first fossil appearances of many animal innovations, including eyes. Animal behavioural complexity increased during this period as well, as evidenced by their traces, suggesting that nervous systems were an innovation of that time. Fossils further suggest that, before 550 MYa, animals were either filter feeders or microbial mat grazers. Extant sponges and Trichoplax perform these tasks using energetically cheaper alternatives than spiking neurones. Genetic evidence testifies that nervous systems evolved before the protostome-deuterostome split. It is less clear whether nervous systems evolved before the cnidarian-bilaterian split, so cnidarians and bilaterians might have evolved their nervous systems independently. The fossil record indicates that the advent of predation could fit into the window of time between those two splits, though molecular clock studies dispute this claim. Collectively, these lines of evidence indicate that animals evolved spiking neurones soon after they started eating each other. The first sensory neurones could have been threshold detectors that spiked in response to other animals in their proximity, alerting them to perform precisely timed actions, such as striking or fleeing.

Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

BACKGROUND

Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria.

RESULTS

Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group.

CONCLUSIONS

Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians

Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested.

Punctuated emergences of genetic and phenotypic innovations in eumetazoan, bilaterian, euteleostome, and hominidae ancestors

Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans, bilaterians, euteleostomi (bony vertebrates), and hominidae, largely specific to each epoch, whereas early branching deuterostome and chordate phyla show very few innovations. Interestingly, groups of proteins that act together in their modern human functions often originated concomitantly, although the corresponding human phenotypes frequently emerged later. For example, the three cnidarians Acropora, Nematostella, and Hydra express a highly similar protein inventory, and their protein innovations can be affiliated either to traits shared by all eumetazoans (gut differentiation, neurogenesis); or to bilaterian traits present in only some cnidarians (eyes, striated muscle); or to traits not identified yet in this phylum (mesodermal layer, endocrine glands). The variable correspondence between phenotypes predicted from protein enrichments and observed phenotypes suggests that a parallel mechanism repeatedly produce similar phenotypes, thanks to novel regulatory events that independently tie preexisting conserved genetic modules.

Transcriptome analysis of the scleractinian coral Stylophora pistillata

The principal architects of coral reefs are the scleractinian corals; these species are divided in two major clades referred to as “robust” and “complex” corals. Although the molecular diversity of the “complex” clade has received considerable attention, with several expressed sequence tag (EST) libraries and a complete genome sequence having been constructed, the “robust” corals have received far less attention, despite the fact that robust corals have been prominent focal points for ecological and physiological studies. Filling this gap affords important opportunities to extend these studies and to improve our understanding of the differences between the two major clades. Here, we present an EST library from Stylophora pistillata (Esper 1797) and systematically analyze the assembled transcripts compared to putative homologs from the complete proteomes of six well-characterized metazoans: Nematostella vectensis, Hydra magnipapillata, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis and Homo sapiens. Furthermore, comparative analyses of the Stylophora pistillata ESTs were performed against several Cnidaria from the Scleractinia, Actiniaria and Hydrozoa, as well as against other stony corals separately. Functional characterization of S. pistillata transcripts into KOG/COG categories and further description of Wnt and bone morphogenetic protein (BMP) signaling pathways showed that the assembled EST library provides sufficient data and coverage. These features of this new library suggest considerable opportunities for extending our understanding of the molecular and physiological behavior of “robust” corals.

A staging system for the regeneration of a polyp from the aboral physa of the anthozoan Cnidarian Nematostella vectensis

BACKGROUND

As the sea anemone Nematostella vectensis emerges as a model for studying regeneration, new tools will be needed to assess its regenerative processes and describe perturbations resulting from experimental investigation. Chief among these is the need for a universal set of staging criteria to establish morphological landmarks that will provide a common format for discussion among investigators.

RESULTS

We have established morphological criteria to describe stages for rapidly assessing regeneration of the aboral end (physa) of Nematostella. Using this staging system, we observed rates of regeneration that are temperature independent during wound healing and temperature dependent afterward. Treatment with 25 μM lipoic acid delays the progression through wound healing without significantly affecting the subsequent rate of regeneration. Also, while an 11-day starvation before amputation causes only a minimal delay in regeneration, this delay is exacerbated by lipoic acid treatment.

CONCLUSIONS

A system for staging the progression of regeneration in amputated Nematostella physa based on easily discernible morphological features provides a standard for the field. This system has allowed us to identify both temperature-dependent and -independent phases of regeneration, as well as a nutritional requirement for normal regenerative progression that is exacerbated by lipoic acid.

The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling

In corals, biocalcification is a major function that may be drastically affected by ocean acidification (OA). Scleractinian corals grow by building up aragonitic exoskeletons that provide support and protection for soft tissues. Although this process has been extensively studied, the molecular basis of biocalcification is poorly understood. Notably lacking is a comprehensive catalog of the skeleton-occluded proteins—the skeletal organic matrix proteins (SOMPs) that are thought to regulate the mineral deposition. Using a combination of proteomics and transcriptomics, we report the first survey of such proteins in the staghorn coral Acropora millepora. The organic matrix (OM) extracted from the coral skeleton was analyzed by mass spectrometry and bioinformatics, enabling the identification of 36 SOMPs. These results provide novel insights into the molecular basis of coral calcification and the macroevolution of metazoan calcifying systems, whereas establishing a platform for studying the impact of OA at molecular level. Besides secreted proteins, extracellular regions of transmembrane proteins are also present, suggesting a close control of aragonite deposition by the calicoblastic epithelium. In addition to the expected SOMPs (Asp/Glu-rich, galaxins), the skeletal repertoire included several proteins containing known extracellular matrix domains. From an evolutionary perspective, the number of coral-specific proteins is low, many SOMPs having counterparts in the noncalcifying cnidarians. Extending the comparison with the skeletal OM proteomes of other metazoans allowed the identification of a pool of functional domains shared between phyla. These data suggest that co-option and domain shuffling may be general mechanisms by which the trait of calcification has evolved.

A framework for the establishment of a cnidarian gene regulatory network for "endomesoderm" specification: the inputs of ß-catenin/TCF signaling

Understanding the functional relationship between intracellular factors and extracellular signals is required for reconstructing gene regulatory networks (GRN) involved in complex biological processes. One of the best-studied bilaterian GRNs describes endomesoderm specification and predicts that both mesoderm and endoderm arose from a common GRN early in animal evolution. Compelling molecular, genomic, developmental, and evolutionary evidence supports the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian ancestor is derived from the same evolutionary precursor of both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals. We have begun to establish the framework of a provisional cnidarian “endomesodermal” gene regulatory network in the sea anemone, Nematostella vectensis, by using a genome-wide microarray analysis on embryos in which the canonical Wnt/ß-catenin pathway was ectopically targeted for activation by two distinct pharmaceutical agents (lithium chloride and 1-azakenpaullone) to identify potential targets of endomesoderm specification. We characterized 51 endomesodermally expressed transcription factors and signaling molecule genes (including 18 newly identified) with fine-scale temporal (qPCR) and spatial (in situ) analysis to define distinct co-expression domains within the animal plate of the embryo and clustered genes based on their earliest zygotic expression. Finally, we determined the input of the canonical Wnt/ß-catenin pathway into the cnidarian endomesodermal GRN using morpholino and mRNA overexpression experiments to show that NvTcf/canonical Wnt signaling is required to pattern both the future endomesodermal and ectodermal domains prior to gastrulation, and that both BMP and FGF (but not Notch) pathways play important roles in germ layer specification in this animal. We show both evolutionary conserved as well as profound differences in endomesodermal GRN structure compared to bilaterians that may provide fundamental insight into how GRN subcircuits have been adopted, rewired, or co-opted in various animal lineages that give rise to specialized endomesodermal cell types.

Cnidarians (anemones, corals, and “jellyfish”) are an animal group whose adults possess derivatives of only two germ layers: ectoderm and a bifunctional (absorptive and contractile) gastrodermal (gut) layer. Cnidarians are the closest living relatives to bilaterally symmetrical animals that possess all three germ layers (ecto, meso, and endoderm); and compelling molecular, genomic, developmental, and evolutionary evidence exists to demonstrate that the cnidarian gastrodermis is evolutionarily related to both endodermal and mesodermal germ layers in all other triploblastic bilaterian animals. Little is known about endomesoderm specification in cnidarians. In this study, we constructed the framework of a cnidarian endomesodermal gene regulatory network in the sea anemone, Nematostella vectensis, using a combination of experimental approaches. We identified and characterized by both qPCR and in situ hybridization 51 genes expressed in defined domains within the presumptive endomesoderm. In addition, we functionally demonstrate that Wnt/Tcf signaling is crucial for regionalized expression of a defined subset of these genes prior to gut formation and endomesoderm maintenance. Our results support the idea of an ancient gene regulatory network underlying endomesoderm specification that involves inputs from multiple signaling pathways (Wnt, FGF, BMP, but not Notch) early in development, that are temporarily uncoupled in bilaterian animals.

The evolution and origin of animal Toll-like receptor signaling pathway revealed by network-level molecular evolutionary analyses

Genes carry out their biological functions through pathways in complex networks consisting of many interacting molecules. Studies on the effect of network architecture on the evolution of individual proteins will provide valuable information for understanding the origin and evolution as well as functional conservation of signaling pathways. However, the relationship between the network architecture and the individual protein sequence evolution is yet little known. In current study, we carried out network-level molecular evolution analysis on TLR (Toll-like receptor ) signaling pathway, which plays an important role in innate immunity in insects and mammals, and we found that: 1) The selection constraint of genes was negatively correlated with its position along TLR signaling pathway; 2) all genes in TLR signaling pathway were highly conserved and underwent strong purifying selection; 3) the distribution of selective pressure along the pathway was driven by differential nonsynonymous substitution levels; 4) The TLR signaling pathway might present in a common ancestor of sponges and eumetazoa, and evolve via the TLR, IKK, IκB and NF-κB genes underwent duplication events as well as adaptor molecular enlargement, and gene structure and conservation motif of NF-κB genes shifted in their evolutionary history. Our results will improve our understanding on the evolutionary history of animal TLR signaling pathway as well as the relationship between the network architecture and the sequences evolution of individual protein.

The evolution of metazoan extracellular matrix

The modular domain structure of extracellular matrix (ECM) proteins and their genes has allowed extensive exon/domain shuffling during evolution to generate hundreds of ECM proteins. Many of these arose early during metazoan evolution and have been highly conserved ever since. Others have undergone duplication and divergence during evolution, and novel combinations of domains have evolved to generate new ECM proteins, particularly in the vertebrate lineage. The recent sequencing of several genomes has revealed many details of this conservation and evolution of ECM proteins to serve diverse functions in metazoa.

Diversity, phylogeny and expression patterns of Pou and Six homeodomain transcription factors in hydrozoan jellyfish Craspedacusta sowerbyi

Formation of all metazoan bodies is controlled by a group of selector genes including homeobox genes, highly conserved across the entire animal kingdom. The homeobox genes from Pou and Six classes are key members of the regulation cascades determining development of sensory organs, nervous system, gonads and muscles. Besides using common bilaterian models, more attention has recently been targeted at the identification and characterization of these genes within the basal metazoan phyla. Cnidaria as a diploblastic sister group to bilateria with simple and yet specialized organs are suitable models for studies on the sensory organ origin and the associated role of homeobox genes. In this work, Pou and Six homeobox genes, together with a broad range of other sensory-specific transcription factors, were identified in the transcriptome of hydrozoan jellyfish Craspedacusta sowerbyi. Phylogenetic analyses of Pou and Six proteins revealed cnidarian-specific sequence motifs and contributed to the classification of individual factors. The majority of the Craspedacusta sowerbyi Pou and Six homeobox genes are predominantly expressed in statocysts, manubrium and nerve ring, the tissues with sensory and nervous activities. The described diversity and expression patterns of Pou and Six factors in hydrozoan jellyfish highlight their evolutionarily conserved functions. This study extends the knowledge of the cnidarian genome complexity and shows that the transcriptome of hydrozoan jellyfish is generally rich in homeodomain transcription factors employed in the regulation of sensory and nervous functions.

Aurelia aurita-Cnidarian with a prominent medusiod stage

Aurelia aurita has a complex life cycle that consists of several stages including alternating generations of medusa and polyps, huge sexual, and tiny asexual stages. Cnidarian is thought to possess two tissue layers: endoderm (gastroderm) and ectoderm, which are separated by mesoglea in medusa. The determination of the composition of the A. aurita jellyfish mesoglea was performed. New protein "mesoglein" was determined as one of the main components of mesoglea. Mesoglein is synthesized by mesogleal cells (Mc), which are populated A. aurita mesoglea as a high molecular mass precursor. Mc are involved in the formation of noncollagenous "elastic" fibers. Deduced amino acid sequence of mesoglein contains Zona Pellucida (ZP) domain and Delta/Serrate/Lag-2 domain. According to reverse transcription PCR, mesoglein is expressed in the mature medusa exclusively in the Mc. The sperm binding to the ZP is particularly important for successful fertilization. Antibodies against mesoglein stain the plate in the place of contact of germinal epithelium and oocyte. The structure found was named the "contact plate." The contact plate could be the precursor of the ZP. All our data suggest that Mc and, probably, the whole mesoglea originate from the epidermis (ectoderm). Computer search for mesoglein relatives reveals Nematostella and Trichoplax proteins as predicted ORFs, indicating that ZP proteins are quite ancient purchase in the evolution.

Evolutionary crossroads in developmental biology: Cnidaria

There is growing interest in the use of cnidarians (corals, sea anemones, jellyfish and hydroids) to investigate the evolution of key aspects of animal development, such as the formation of the third germ layer (mesoderm), the nervous system and the generation of bilaterality. The recent sequencing of the Nematostella and Hydra genomes, and the establishment of methods for manipulating gene expression, have inspired new research efforts using cnidarians. Here, we present the main features of cnidarian models and their advantages for research, and summarize key recent findings using these models that have informed our understanding of the evolution of the developmental processes underlying metazoan body plan formation.

A conserved germline multipotency program

The germline of multicellular animals is segregated from somatic tissues, which is an essential developmental process for the next generation. Although certain ecdysozoans and chordates segregate their germline during embryogenesis, animals from other taxa segregate their germline after embryogenesis from multipotent progenitor cells. An overlapping set of genes, including vasa, nanos and piwi, operate in both multipotent precursors and in the germline. As we propose here, this conservation implies the existence of an underlying germline multipotency program in these cell types that has a previously underappreciated and conserved function in maintaining multipotency.

Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata

Projected elevation of seawater temperatures poses a threat to the reproductive success of Caribbean reef-building corals that have planktonic development during the warmest months of the year. This study examined the transcriptomic changes that occurred during embryonic and larval development of the elkhorn coral, Acropora palmata, at a non-stressful temperature (28°C) and further assessed the effects of two elevated temperatures (30°C and 31.5°C) on these expression patterns. Using cDNA microarrays, we compared expression levels of 2051 genes from early embryos and larvae at multiple developmental stages (including pre-blastula, blastula, gastrula, and planula stages) at each of the three temperatures. At 12h post-fertilization in 28°C treatments, genes involved in cell replication/cell division and transcription were up-regulated in A. palmata embryos, followed by a reduction in expression of these genes during later growth stages. From 24.5 to 131h post-fertilization at 28°C, A. palmata altered its transcriptome by up-regulating genes involved in protein synthesis and metabolism. Temperatures of 30°C and 31.5°C caused major changes to the A. palmata embryonic transcriptomes, particularly in the samples from 24.5hpf post-fertilization, characterized by down-regulation of numerous genes involved in cell replication/cell division, metabolism, cytoskeleton, and transcription, while heat shock genes were up-regulated compared to 28°C treatments. These results suggest that increased temperature may cause a breakdown in proper gene expression during development in A. palmata by down-regulation of genes involved in essential cellular processes, which may lead to the abnormal development and reduced survivorship documented in other studies.

Early origin of the bilaterian developmental toolkit

Whole-genome sequences from the choanoflagellate Monosiga brevicollis, the placozoan Trichoplax adhaerens and the cnidarian Nematostella vectensis have confirmed results from comparative evolutionary developmental studies that much of the developmental toolkit once thought to be characteristic of bilaterians appeared much earlier in the evolution of animals. The diversity of transcription factors and signalling pathway genes in animals with a limited number of cell types and a restricted developmental repertoire is puzzling, particularly in light of claims that such highly conserved elements among bilaterians provide evidence of a morphologically complex protostome-deuterostome ancestor. Here, I explore the early origination of elements of what became the bilaterian toolkit, and suggest that placozoans and cnidarians represent a depauperate residue of a once more diverse assemblage of early animals, some of which may be represented in the Ediacaran fauna (c. 585-542 Myr ago).

Photoreactivation is the main repair pathway for UV-induced DNA damage in coral planulae

The larvae of most coral species spend some time in the plankton, floating just below the surface and hence exposed to high levels of ultraviolet radiation (UVR). The high levels of UVR are potentially stressful and damaging to DNA and other cellular components, such as proteins, reducing survivorship. Consequently, mechanisms to either shade (prevent) or repair damage potentially play an important role. In this study, the role of photoreactivation in the survival of coral planulae was examined. Photoreactivation is a light-stimulated response to UV-damaged DNA in which photolyase proteins repair damaged DNA. Photoreactivation rates, as well as the localization of photolyase, were explored in planulae under conditions where photoreactivation was or was not inhibited. The results indicate that photoreactivation is the main DNA repair pathway in coral planulae, repairing UV-induced DNA damage swiftly (K=1.75 h–1 and a half-life of repair of 23 min), with no evidence of any light-independent DNA repair mechanisms, such as nucleotide excision repair (NER), at work. Photolyase mRNA was localized to both the ectoderm and endoderm of the larvae. The amount of cell death in the coral planulae increased significantly when photoreactivation was inhibited, by blocking photoreactivating light. We found that photoreactivation, along with additional UV shielding in the form of five mycosporine-like amino acids, are sufficient for survival in surface tropical waters and that planulae do not accumulate DNA damage despite being exposed to high UVR.

Cnidarians and the evolutionary origin of the nervous system

Cnidarians are widely regarded as one of the first organisms in animal evolution possessing a nervous system. Conventional histological and electrophysiological studies have revealed a considerable degree of complexity of the cnidarian nervous system. Thanks to expressed sequence tags and genome projects and the availability of functional assay systems in cnidarians, this simple nervous system is now genetically accessible and becomes particularly valuable for understanding the origin and evolution of the genetic control mechanisms underlying its development. In the present review, the anatomical and physiological features of the cnidarian nervous system and the interesting parallels in neurodevelopmental mechanisms between Cnidaria and Bilateria are discussed.

Multiple dicer genes in the early-diverging metazoa

Dicer proteins are highly conserved, are present in organisms ranging from plants to metazoans, and are essential components of the RNA interference pathway. Although the complement of Dicer proteins has been investigated in many "higher" metazoans, there has been no corresponding characterization of Dicer proteins in any early-branching metazoan. We cloned partial cDNAs of genes belonging to the Dicer family from the anthozoan cnidarian Nematostella vectensis and two distantly related haplotypes (species lineages) of the Placozoa (Trichoplax adhaerens 16S haplotype 1 [H1] and Placozoa sp. [H2]). We also identified Dicer genes in the hydrozoan Hydra magnipapillata and the demosponge Amphimedon queenslandica with the use of publicly available sequence databases. Two Dicer genes are present in each cnidarian species, whereas five Dicer genes each are found in the Porifera and Placozoa. Phylogenetic analyses comparing these and other metazoan Dicers suggest an ancient duplication event of a "Proto-Dicer" gene. We show that the Placozoa is the only known metazoan phylum which contains both representatives of this duplication event and that the multiple Dicer genes of the "basal" metazoan phyla represent lineage-specific duplications. There is a striking diversity of Dicer genes in basal metazoans, in stark contrast to the single Dicer gene found in most higher metazoans. This new data has allowed us to formulate new hypotheses regarding the evolution of metazoan Dicer proteins and their possible functions in the early diverging metazoan phyla. We theorize that the multiple placozoan Dicer genes fulfill a specific biological requirement, such as an immune defense strategy against viruses.

Roles of calmodulin and calcium/calmodulin-dependent protein kinase in flagellar motility regulation in the coral Acropora digitifera

In the corals Acropora spp., eggs secrete substances that induce sperm motility regulation. An elevation of intracellular pH ([pH]i) and a regulation of intracellular Ca(2+) concentration ([Ca(2+)]) are involved in the sperm motility regulation cascade. However, the detailed molecular aspects of flagellar motility regulation have not been fully demonstrated in Acropora. In this study, we determined the presence and roles of both calmodulin (CaM) and calcium/calmodulin dependent-protein kinase (CaMK) in the sperm flagellar motility regulation of Acropora. A (45)Ca(2+)-overlay assay and an immunoblot analysis showed that sperm contain an acidic 16-kDa protein that was CaM, and an immunoblot analysis revealed the presence of CaMK in coral sperm. In addition, a specific inhibitor of CaMK, KN-93, and a CaM antagonist, W-7, inhibited sperm motility activation induced by NH(4)Cl treatment. NH(4)Cl treatment causes an increase in intracellular [pH]i of sperm, suggesting that CaM and CaMK are involved in sperm motility initiation caused by an increase in [pH]i. The involvement of CaM and CaMK in motility regulation in coral highlights the importance of these molecules throughout the animal kingdom.

Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa

Background

Sox genes encode transcription factors that function in a wide range of developmental processes across the animal kingdom. To better understand both the evolution of the Sox family and the roles of these genes in cnidarians, we are studying the Sox gene complement of the coral, Acropora millepora (Class Anthozoa).

Results

Based on overall domain structures and HMG box sequences, the Acropora Sox genes considered here clearly fall into four of the five major Sox classes. AmSoxC is expressed in the ectoderm during development, in cells whose morphology is consistent with their assignment as sensory neurons. The expression pattern of the Nematostella ortholog of this gene is broadly similar to that of AmSoxC, but there are subtle differences – for example, expression begins significantly earlier in Acropora than in Nematostella. During gastrulation, AmSoxBb and AmSoxB1 transcripts are detected only in the presumptive ectoderm while AmSoxE1 transcription is restricted to the presumptive endoderm, suggesting that these Sox genes might play roles in germ layer specification. A third type B Sox gene, AmSoxBa, and a Sox F gene AmSoxF also have complex and specific expression patterns during early development. Each of these genes has a clear Nematostella ortholog, but in several cases the expression pattern observed in Acropora differs significantly from that reported in Nematostella.

Conclusion

These differences in expression patterns between Acropora and Nematostella largely reflect fundamental differences in developmental processes, underscoring the diversity of mechanisms within the anthozoan Sub-Class Hexacorallia (Zoantharia).

Unexpected diversity of cnidarian integrins: expression during coral gastrulation

BACKGROUND

Adhesion mediated through the integrin family of cell surface receptors is central to early development throughout the Metazoa, playing key roles in cell-extra cellular matrix adhesion and modulation of cadherin activity during the convergence and extension movements of gastrulation. It has been suggested that Caenorhabditis elegans, which has a single beta and two alpha integrins, might reflect the ancestral integrin complement. Investigation of the integrin repertoire of anthozoan cnidarians such as the coral Acropora millepora is required to test this hypothesis and may provide insights into the original roles of these molecules.

RESULTS

Two novel integrins were identified in Acropora. AmItgalpha1 shows features characteristic of alpha integrins lacking an I-domain, but phylogenetic analysis gives no clear indication of its likely binding specificity. AmItgbeta2 lacks consensus cysteine residues at positions 8 and 9, but is otherwise a typical beta integrin. In situ hybridization revealed that AmItgalpha1, AmItgbeta1, and AmItgbeta2 are expressed in the presumptive endoderm during gastrulation. A second anthozoan, the sea anemone Nematostella vectensis, has at least four beta integrins, two resembling AmItgbeta1 and two like AmItgbeta2, and at least three alpha integrins, based on its genomic sequence.

CONCLUSION

In two respects, the cnidarian data do not fit expectations. First, the cnidarian integrin repertoire is more complex than predicted: at least two betas in Acropora, and at least three alphas and four betas in Nematostella. Second, whereas the bilaterian alphas resolve into well-supported groups corresponding to those specific for RGD-containing or laminin-type ligands, the known cnidarian alphas are distinct from these. During early development in Acropora, the expression patterns of the three known integrins parallel those of amphibian and echinoderm integrins.

Evolution of polydom-like molecules: identification and characterization of cnidarian polydom (Cnpolydom) in the basal metazoan Hydractinia

End sequencing of random BAC clones from a Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa) genomic library revealed a gene across a approximately 37.5kb region of the H. symbiolongicarpus genome sharing highest sequence identity and domain architecture to mammalian polydom that we in turn named cnidarian polydom (CnPolydom). Sharing all eight domain types characteristic of polydom and organized in a similar 5'-3' manner, CnPolydom was predicted to contain three additional domain types: PAN, FA58C, and CUB that are characteristic of CnPolydom. Expression analysis of CnPolydom from H. symbiolongicarpus (Hysy-CnPolydom) showed upregulation in response to bacterial and primarily fungal challenges, with transcripts produced specifically by a subset of interstitial stem cells (i-cells) and/or neural cells throughout the ectodermal tissue layer of feeding polyps (gastrozooids). This is the first description of a polydom-like molecule outside of Mammalia and provides evolutionary perspective on the ancestral structure and role of this pentraxin family clade.