Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis

Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora

Background

Scleractinian corals of the genus Montipora (Anthozoa, Cnidaria) possess some unusual biological traits, such as vertical transmission of algal symbionts; however, the genetic bases for those traits remain unknown. We performed extensive comparative genomic analyses among members of the family Acroporidae (Montipora, Acropora, and Astreopora) to explore genomic novelties that might explain unique biological traits of Montipora using improved genome assemblies and gene predictions for M. cactus, M. efflorescens and Astreopora myriophthalma.

Results

We obtained genomic data for the three species of comparable high quality to other published coral genomes. Comparative genomic analyses revealed that the gene families restricted to Montipora are significantly more numerous than those of Acropora and Astreopora, but their functions are largely unknown. The number of gene families specifically expanded in Montipora was much lower than the number specifically expanded in Acropora. In addition, we found that evolutionary rates of the Montipora-specific gene families were significantly higher than other gene families shared with Acropora and/or Astreopora. Of 40 gene families under positive selection (Ka/Ks ratio > 1) in Montipora, 30 were specifically detected in Montipora-specific gene families. Comparative transcriptomic analysis of early life stages of Montipora, which possesses maternally inherited symbionts, and Acropora, which lacks them, revealed that most gene families continuously expressed in Montipora, but not expressed in Acropora do not have orthologs in Acropora. Among the 30 Montipora-specific gene families under positive selection, 27 are expressed in early life stages.

Conclusions

Lineage-specific gene families were important to establish the genus Montipora, particularly genes expressed throughout early life stages, which under positive selection, gave rise to biological traits unique to Montipora. Our findings highlight evolutionarily acquired genomic bases that may support symbiosis in these stony corals and provide novel insights into mechanisms of coral-algal symbiosis, the physiological foundation of coral reefs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02023-8.

Temperature regulates the recognition activities of a galectin to pathogen and symbiont in the scleractinian coral Pocillopora damicornis

Lectins serve as essential pattern recognition receptors, and play important roles in the recognition of non-self and mediation of innate immune response in metazoans. Scleractinian corals are vulnerable to pathogen infection and endosymbiosis disruption under heat stress that can finally lead to coral bleaching. In this study, a cDNA sequence encoding one galectin was cloned in scleractinian coral Pocillopora damicornis (PdGLT-1). The deduced PdGLT-1 protein shared highest amino acid sequence similarity (99%) with galectin from Stylophora pistillata (XP_022806650.1), and was composed of one signal peptide, one Collagen domain and one Gal-Lectin domain. PdGLT-1 recombinant protein (rPdGLT-1) was expressed and purified in vitro. Binding activities of rPdGLT-1 to bacteria and symbiont were determined using western blotting method. Results showed that rPdGLT-1 was able to bind to gram-positive bacterium Streptococcus mutans, gram-negative bacteria Vibrio coralliilyticus and Escherichia coli, with the highest activity for V. coralliilyticus, and further agglutinated them. The bound rPdGLT-1 to Symbiodinium (10-10⁴ cells mL^-1) was detectable, and its binding ability was concentration-dependent. Furthermore, dual binding activities were determined under different temperatures (20, 25, 30 and 35 °C), and the optimal temperatures were found to be 25 and 30 °C for V. coralliilyticus and Symbiodinium, respectively. Results suggested that PdGLT-1 could recognize pathogenic bacteria and symbiotic dinoflagellates Symbiodinium. However, their recognition activities were repressed under high temperature (>30 °C). This study provided insights into the underlying mechanism of lectin modulation to heat bleaching through its pathogen and Symbiodinium recognition in the scleractinian coral P. damicornis.

Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species

Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.

Effects of environmental factors on C-type lectin recognition to zooxanthellae in the stony coral Pocillopora damicornis

C-type lectin is a superfamily of Ca²⁺-dependent carbohydrate-recognition proteins that play significant roles in nonself-recognition and pathogen clearance. In the present study, a C-type lectin (PdC-Lectin) was chosen from stony coral Pocillopora damicornis to understand its recognition characteristics to zooxanthellae. PdC-Lectin protein contained a signal peptide and a carbohydrate-recognition domain with EPN motif in Ca²⁺-binding site 2. The PdC-Lectin recombinant protein was expressed and purified in vitro. The binding of PdC-Lectin protein to zooxanthellae was determined with western blotting method, and the bound protein to 10-10⁵ cell mL^-1 zooxanthellae was detectable in a concentration-dependent manner. Less PdC-Lectin protein binding to zooxanthellae was observed for the incubation at 36 °C than that at 26 °C. Furthermore, the PAMP recognition spectrum of PdC-Lectin protein was tested through surface plasmon resonance method, and it bound to LPS and Lipid A, but not to LTA, β-glucan, mannose or Poly (I:C). When PdC-Lectin protein was preincubated with LPS, there was less protein binding to zooxanthellae compared with that in non-preincubation group. These results collectively suggest that PdC-Lectin could recognize zooxanthellae, and the recognition could be repressed by high temperature and pathogenic bacteria, which would help to further understand the molecular mechanism of coral bleaching and the establishment of coral-zooxanthella symbiosis in the stony coral P. damicornis.

Dual recognition activity of a rhamnose-binding lectin to pathogenic bacteria and zooxanthellae in stony coral Pocillopora damicornis

Rhamnose-binding lectin (RBL) is a type of Ca²⁺-independent lectin with tandem repeat carbohydrate-recognition domain, and is crucial for the innate immunity in many invertebrates. In this study, the cDNA sequence encoding RBL in coral Pocillopora damicornis (PdRBL-1) was cloned. The PdRBL-1 protein shared highest amino acid sequence similarity (55%) with the polyp of Hydra vulgaris, and contained a signal peptide and two tandem carbohydrate-recognition domains in which all cysteine residues were conserved. Surface plasmon resonance method revealed that the recombinant PdRBL-1 protein bound to LPS and Lipid A, but not to LTA, β-glucan, mannose and Poly (I:C). Results also showed that it bonded with zooxanthellae using western blotting method, and that the bound protein was detectable only at concentrations higher than 10² zooxanthellae cell mL^-1. When recombinant PdRBL-1 protein was preincubated with LPS, lower amounts of protein bound to zooxanthellae compared to cells not preincubated with LPS. Furthermore, PdRBL-1 mRNA expression increased significantly at 12 h, and declined to the baseline at 24 h after heat stress at 31 °C. These results collectively suggest that PdRBL-1 could recognize not only pathogenic bacteria but also symbiotic zooxanthellae, and that the recognition of zooxanthellae by PdRBL-1 could be repressed by pathogenic bacteria through competitive binding. This information allows us to gain new insights in the mechanisms influencing the establishment and maintenance of coral-zooxanthella symbiosis in coral P. damicornis.

Do photobiont switch and cephalodia emancipation act as evolutionary drivers in the lichen symbiosis? A case study in the Pannariaceae (Peltigerales)

Lichen symbioses in the Pannariaceae associate an ascomycete and either cyanobacteria alone (usually Nostoc; bipartite thalli) or green algae and cyanobacteria (cyanobacteria being located in dedicated structures called cephalodia; tripartite thalli) as photosynthetic partners (photobionts). In bipartite thalli, cyanobacteria can either be restricted to a well-delimited layer within the thallus ('pannarioid' thalli) or spread over the thallus that becomes gelatinous when wet ('collematoid' thalli). We studied the collematoid genera Kroswia and Physma and an undescribed tripartite species along with representatives of the pannarioid genera Fuscopannaria, Pannaria and Parmeliella. Molecular inferences from 4 loci for the fungus and 1 locus for the photobiont and statistical analyses within a phylogenetic framework support the following: (a) several switches from pannarioid to collematoid thalli occured and are correlated with photobiont switches; the collematoid genus Kroswia is nested within the pannarioid genus Fuscopannaria and the collematoid genus Physma is sister to the pannarioid Parmeliella mariana group; (b) Nostoc associated with collematoid thalli in the Pannariaceae are related to that of the Collemataceae (which contains only collematoid thalli), and never associated with pannarioid thalli; Nostoc associated with pannarioid thalli also associate in other families with similar morphology; (c) ancestors of several lineages in the Pannariaceae developed tripartite thalli, bipartite thalli probably resulting from cephalodia emancipation from tripartite thalli which eventually evolved and diverged, as suggested by the same Nostoc present in the collematoid genus Physma and in the cephalodia of a closely related tripartite species; Photobiont switches and cephalodia emancipation followed by divergence are thus suspected to act as evolutionary drivers in the family Pannariaceae.

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.

Adhesion networks of cnidarians: a postgenomic view

Cell-extracellular matrix (ECM) and cell-cell adhesion systems are fundamental to the multicellularity of metazoans. Members of phylum Cnidaria were classified historically by their radial symmetry as an outgroup to bilaterian animals. Experimental study of Hydra and jellyfish has fascinated zoologists for many years. Laboratory studies, based on dissection, biochemical isolations, or perturbations of the living organism, have identified the ECM layer of cnidarians (mesoglea) and its components as important determinants of stem cell properties, cell migration and differentiation, tissue morphogenesis, repair, and regeneration. Studies of the ultrastructure and functions of intercellular gap and septate junctions identified parallel roles for these structures in intercellular communication and morphogenesis. More recently, the sequenced genomes of sea anemone Nematostella vectensis, Hydra magnipapillata, and coral Acropora digitifera have opened up a new frame of reference for analyzing the cell-ECM and cell-cell adhesion molecules of cnidarians and examining their conservation with bilaterians. This chapter integrates a review of literature on the structure and functions of cell-ECM and cell-cell adhesion systems in cnidarians with current analyses of genome-encoded repertoires of adhesion molecules. The postgenomic perspective provides a fresh view on fundamental similarities between cnidarian and bilaterian animals and is impelling wider adoption of species from phylum Cnidaria as model organisms.

Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation

To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochondrial sequence data implied contemporary range size and vulnerability are linked to species age. However, contrary to previous hypotheses that suggest geographically restricted Acropora species evolved in the Plio-Pleistocene, the molecular phylogeny depicts some Indo-Australian species have greater antiquity, diverging in the Miocene. Species age is not related to range size as a simple positive linear function and interpreting the precise tempo of evolution in this genus is greatly complicated by morphological homoplasy and a sparse fossil record. Our phylogenetic reconstructions provide new examples of how morphology conceals cryptic evolutionary relationships in this keystone genus, and offers limited support for the species groupings currently used in Acropora systematics. We hypothesize that in addition to age, other mechanisms (such as a reticulate ancestry) delimit the contemporary range of some Acropora species, as evidenced by the complex patterns of allele sharing and paraphyly we uncover. Overall, both new and ancient evolutionary information may be lost if geographically restricted and threatened Acropora species are forced to extinction. In order to protect coral biodiversity and resolve the evolutionary history of staghorn coral, further analyses based on comprehensive and heterogeneous morphological and molecular data utilizing reticulate models of evolution are needed.

Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases

Over the last decade, significant advances have been made in characterization of the coral microbiota. Shifts in its composition often correlate with the appearance of signs of diseases and/or bleaching, thus suggesting a link between microbes, coral health and stability of reef ecosystems. The understanding of interactions in coral-associated microbiota is informed by the on-going characterization of other microbiomes, which suggest that metabolic pathways and functional capabilities define the 'core' microbiota more accurately than the taxonomic diversity of its members. Consistent with this hypothesis, there does not appear to be a consensus on the specificity in the interactions of corals with microbial commensals, even though recent studies report potentially beneficial functions of the coral-associated bacteria. They cycle sulphur, fix nitrogen, produce antimicrobial compounds, inhibit cell-to-cell signalling and disrupt virulence in opportunistic pathogens. While their beneficial functions have been documented, it is not certain whether or how these microbes are selected by the hosts. Therefore, understanding the role of innate immunity, signal and nutrient exchange in the establishment of coral microbiota and in controlling its functions will probably reveal ancient, evolutionarily conserved mechanisms that dictate the outcomes of host-microbial interactions, and impact the resilience of the host.

LEC-2, a highly variable lectin in the lichen Peltigera membranacea

Lectins are a diverse group of carbohydrate binding proteins often involved in cellular interactions. A lectin gene, lec-2, was identified in the mycobiont of the lichen Peltigera membranacea. Sequencing of lec-2 open reading frames from 21 individual samples showed an unexpectedly high level of polymorphism in the deduced protein (LEC-2), which was sorted into nine haplotypes based on amino acid sequence. Calculations showed that the rates of nonsynonymous versus synonymous nucleotide substitutions deviated significantly from the null hypothesis of neutrality, indicating strong positive selection. Molecular modeling revealed that most amino acid replacements were around the putative carbohydrate-binding pocket, indicating changes in ligand binding. Lectins have been thought to be involved in the recognition of photobiont partners in lichen symbioses, and the hypothesis that positive selection of LEC-2 is driven by variation in the Nostoc photobiont partner was tested by comparing mycobiont LEC-2 haplotypes and photobiont genotypes, as represented by the rbcLX region. It was not possible to pair up the two types of marker sequences without conflicts, suggesting that positive selection of LEC-2 was not due to variation in photobiont partners.

Study of cnidarian-algal symbiosis in the "omics" age

The symbiotic associations between cnidarians and dinoflagellate algae (Symbiodinium) support productive and diverse ecosystems in coral reefs. Many aspects of this association, including the mechanistic basis of host-symbiont recognition and metabolic interaction, remain poorly understood. The first completed genome sequence for a symbiotic anthozoan is now available (the coral Acropora digitifera), and extensive expressed sequence tag resources are available for a variety of other symbiotic corals and anemones. These resources make it possible to profile gene expression, protein abundance, and protein localization associated with the symbiotic state. Here we review the history of "omics" studies of cnidarian-algal symbiosis and the current availability of sequence resources for corals and anemones, identifying genes putatively involved in symbiosis across 10 anthozoan species. The public availability of candidate symbiosis-associated genes leaves the field of cnidarian-algal symbiosis poised for in-depth comparative studies of sequence diversity and gene expression and for targeted functional studies of genes associated with symbiosis. Reviewing the progress to date suggests directions for future investigations of cnidarian-algal symbiosis that include (i) sequencing of Symbiodinium, (ii) proteomic analysis of the symbiosome membrane complex, (iii) glycomic analysis of Symbiodinium cell surfaces, and (iv) expression profiling of the gastrodermal cells hosting Symbiodinium.

Expression of putative immune response genes during early ontogeny in the coral Acropora millepora

BACKGROUND

Corals, like many other marine invertebrates, lack a mature allorecognition system in early life history stages. Indeed, in early ontogeny, when corals acquire and establish associations with various surface microbiota and dinoflagellate endosymbionts, they do not efficiently distinguish between closely and distantly related individuals from the same population. However, very little is known about the molecular components that underpin allorecognition and immunity responses or how they change through early ontogeny in corals.

METHODOLOGY/PRINCIPAL FINDINGS

Patterns in the expression of four putative immune response genes (apextrin, complement C3, and two CELIII type lectin genes) were examined in juvenile colonies of Acropora millepora throughout a six-month post-settlement period using quantitative real-time PCR (qPCR). Expression of a CELIII type lectin gene peaked in the fourth month for most of the coral juveniles sampled and was significantly higher at this time than at any other sampling time during the six months following settlement. The timing of this increase in expression levels of putative immune response genes may be linked to allorecognition maturation which occurs around this time in A. millepora. Alternatively, the increase may represent a response to immune challenges, such as would be involved in the recognition of symbionts (such as Symbiodinium spp. or bacteria) during winnowing processes as symbioses are fine-tuned.

CONCLUSIONS/SIGNIFICANCE

Our data, although preliminary, are consistent with the hypothesis that lectins may play an important role in the maturation of allorecognition responses in corals. The co-expression of lectins with apextrin during development of coral juveniles also raises the possibility that these proteins, which are components of innate immunity in other invertebrates, may influence the innate immune systems of corals through a common pathway or system. However, further studies investigating the expression of these genes in alloimmune-challenged corals are needed to further clarify emerging evidence of a complex innate immunity system in corals.

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals

Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts.

Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.

Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome

Background

Cnidarians, including corals and anemones, offer unique insights into metazoan evolution because they harbor genetic similarities with vertebrates beyond that found in model invertebrates and retain genes known only from non-metazoans. Cataloging genes expressed in Acropora palmata, a foundation-species of reefs in the Caribbean and western Atlantic, will advance our understanding of the genetic basis of ecologically important traits in corals and comes at a time when sequencing efforts in other cnidarians allow for multi-species comparisons.

Results

A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences. Analysis of the assembled sequences indicated that 83–100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (∼18,000–20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals.

Conclusions

Currently available transcriptome data now make comparative studies of the mechanisms underlying coral's evolutionary success possible. Here we identified candidate genes that enable corals to maintain genomic integrity despite considerable exposure to genotoxic stress over long life spans, and showed conservation of important physiological pathways between corals and bilaterians.