Rapid evolution of coral proteins responsible for interaction with the environment.

BACKGROUND: Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably. METHODOLOGY/PRINCIPAL FINDINGS: We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium. CONCLUSION/RELEVANCE: This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.

Circadian clock gene expression in the coral Favia fragum over diel and lunar reproductive cycles.

Natural light cycles synchronize behavioral and physiological cycles over varying time periods in both plants and animals. Many scleractinian corals exhibit diel cycles of polyp expansion and contraction entrained by diel sunlight patterns, and monthly cycles of spawning or planulation that correspond to lunar moonlight cycles. The molecular mechanisms for regulating such cycles are poorly understood. In this study, we identified four molecular clock genes (cry1, cry2, clock and cycle) in the scleractinian coral, Favia fragum, and investigated patterns of gene expression hypothesized to be involved in the corals' diel polyp behavior and lunar reproductive cycles. Using quantitative PCR, we measured fluctuations in expression of these clock genes over both diel and monthly spawning timeframes. Additionally, we assayed gene expression and polyp expansion-contraction behavior in experimental corals in normal light:dark (control) or constant dark treatments. Well-defined and reproducible diel patterns in cry1, cry2, and clock expression were observed in both field-collected and the experimental colonies maintained under control light:dark conditions, but no pattern was observed for cycle. Colonies in the control light:dark treatment also displayed diel rhythms of tentacle expansion and contraction. Experimental colonies in the constant dark treatment lost diel patterns in cry1, cry2, and clock expression and displayed a diminished and less synchronous pattern of tentacle expansion and contraction. We observed no pattern in cry1, cry2, clock, or cycle expression correlated with monthly spawning events suggesting these genes are not involved in the entrainment of reproductive cycles to lunar light cycles in F. fragum. Our results suggest a molecular clock mechanism, potentially similar to that in described in fruit flies, exists within F. fragum.

Location-specific responses to thermal stress in larvae of the reef-building coral Montastraea faveolata.

BACKGROUND: The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. METHODOLOGY/PRINCIPAL FINDINGS: To test the hypothesis that larval transcription profiles reflect location-specific responses to thermal stress, symbiont-free gametes from three to four colonies of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico, fertilized, and raised under mean and elevated (up 1 to 2 degrees C above summer mean) temperatures. These locations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among 1,310 unigenes were simultaneously characterized using custom cDNA microarrays, allowing investigation of gene expression patterns among larvae generated from wild populations under stress. Results show both conserved and location-specific variation in key processes including apoptosis, cell structuring, adhesion and development, energy and protein metabolism, and response to stress, in embryos of a reef-building coral. CONCLUSIONS/SIGNIFICANCE: These results provide first insights into location-specific variation in gene expression in the face of gene flow, and support the hypothesis that coral host genomes may house adaptive potential needed to deal with changing environmental conditions.

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.

Elevated temperature affects development, survivorship, and settlement of the elkhorn coral, Acropora palmata (Lamarck 1816).

Elevated seawater temperatures during the late summer have the potential to negatively affect the development and survivorship of the larvae of reef corals that are reproductive during that time of year. Acropora palmata, a major Caribbean hermatype, reproduces annually during August and September. A. palmata populations have severely declined over the past three decades, and recovery will require high recruitment rates. Such recruitment will be limited if larval supply is reduced by elevated temperatures. The effects of elevated temperatures on development, survival, and larval settlement of A. palmata were investigated by culturing newly fertilized eggs at temperatures ranging from 27.5 to 31.5 degrees C. Development was accelerated and the percentage of developmental abnormalities increased at higher temperatures. Embryo mortality peaked during gastrulation, indicating that this complex developmental process is particularly sensitive to elevated temperatures. Larvae cultured at 30 and 31.5 degrees C experienced as much as an 8-fold decrease in survivorship compared to those at 28 degrees C. Additionally, settlement was 62% at 28 degrees C compared to 37% at 31.5 degrees C. These results indicate that embryos and larvae of A. palmata will be negatively affected as sea surface temperatures continue to warm, likely reducing recruitment and the recovery potential of A. palmata on Caribbean reefs.

Effects of temperature on gene expression in embryos of the coral Montastraea faveolata.

BACKGROUND: Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5 degrees C, 29.0 degrees C, and 31.5 degrees C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours. RESULTS: Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the long-term regulation upon heat stress. CONCLUSIONS: Embryos responded differently depending on exposure time and temperature level. Embryos showed expression of stress-related genes already at a temperature of 29.0 degrees C, but seemed to be able to counteract the initial response over time. By contrast, embryos at 31.5 degrees C displayed continuous expression of stress genes. The genes that played a role in the response to elevated temperatures consisted of both highly conserved and coral-specific genes. These genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change.

The host transcriptome remains unaltered during the establishment of coral-algal symbioses.

Coral reefs are based on the symbiotic relationship between corals and photosynthetic dinoflagellates of the genus Symbiodinium. We followed gene expression of coral larvae of Acropora palmata and Montastraea faveolata after exposure to Symbiodinium strains that differed in their ability to establish symbioses. We show that the coral host transcriptome remains almost unchanged during infection by competent symbionts, but is massively altered by symbionts that fail to establish symbioses. Our data suggest that successful coral-algal symbioses depend mainly on the symbionts' ability to enter the host in a stealth manner rather than a more active response from the coral host.

Gene expression microarray analysis encompassing metamorphosis and the onset of calcification in the scleractinian coral Montastraea faveolata.

Similar to many marine invertebrates, scleractinian corals experience a dramatic morphological transformation, as well as a habitat switch, upon settlement and metamorphosis. At this time, planula larvae transform from non-calcifying, demersal, motile organisms into sessile, calcifying, benthic juvenile polyps. We performed gene expression microarray analyses between planulae, aposymbiotic primary polyps, and symbiotic adult tissue to elucidate the molecular mechanisms underlying coral metamorphosis and early stages of calcification in the Robust/Short clade scleractinian coral Montastraea faveolata. Among the annotated genes, the most abundant upregulated transcripts in the planula stage are involved in protein synthesis, chromatin assembly and mitochondrial metabolism; the polyp stage, morphogenesis, protein catabolism and organic matrix synthesis; and the adult stage, sexual reproduction, stress response and symbiosis. We also present evidence showing that the planula and adult transcriptomes are more similar to each other than to the polyp transcriptome. Our results also point to a large number of uncharacterized adult coral-specific genes likely involved in coral-specific functions such as symbiosis and calcification.

Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.

BACKGROUND: Scleractinian corals are the foundation of reef ecosystems in tropical marine environments. Their great success is due to interactions with endosymbiotic dinoflagellates (Symbiodinium spp.), with which they are obligately symbiotic. To develop a foundation for studying coral biology and coral symbiosis, we have constructed a set of cDNA libraries and generated and annotated ESTs from two species of corals, Acropora palmata and Montastraea faveolata. RESULTS: We generated 14,588 (Ap) and 3,854 (Mf) high quality ESTs from five life history/symbiosis stages (spawned eggs, early-stage planula larvae, late-stage planula larvae either infected with symbionts or uninfected, and adult coral). The ESTs assembled into a set of primarily stage-specific clusters, producing 4,980 (Ap), and 1,732 (Mf) unigenes. The egg stage library, relative to the other developmental stages, was enriched in genes functioning in cell division and proliferation, transcription, signal transduction, and regulation of protein function. Fifteen unigenes were identified as candidate symbiosis-related genes as they were expressed in all libraries constructed from the symbiotic stages and were absent from all of the non symbiotic stages. These include several DNA interacting proteins, and one highly expressed unigene (containing 17 cDNAs) with no significant protein-coding region. A significant number of unigenes (25) encode potential pattern recognition receptors (lectins, scavenger receptors, and others), as well as genes that may function in signaling pathways involved in innate immune responses (toll-like signaling, NFkB p105, and MAP kinases). Comparison between the A. palmata and an A. millepora EST dataset identified ferritin as a highly expressed gene in both datasets that appears to be undergoing adaptive evolution. Five unigenes appear to be restricted to the Scleractinia, as they had no homology to any sequences in the nr databases nor to the non-scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata. CONCLUSION: Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

THE EFFECTS OF SALINITY STRESS ON THE RATES OF AEROBIC RESPIRATION AND PHOTOSYNTHESIS IN THE HERMATYPIC CORAL SIDERASTREA SIDEREA.

Corals are reputed to have low tolerance to salinity fluctuations. Yet the scleractinian coral Siderastrea siderea commonly inhabits reef zones and nearshore areas that experience salinity fluctuations of 5 to l0%. Small colonies of this species were subjected to both long-term and sudden decreases or increases in salinity. Their rates of aerobic respiration and photosynthesis, measured as changes in oxygen concentration, were followed for up to 144 hours after the sudden changes. Normal salinities of coastal waters near Panacea, Florida, are 28 to 30% but S. siderea was able to acclimate to 42% when salinity was increased slowly over a 30-day period. Neither respiratory nor photosynthetic rates of S. siderea were affected by changes in salinity of less than 10% above or below the acclimation salinity. Greater changes in salinity (either up or down) caused decreases in respiratory and photosynthetic rates proportional to the magnitude of the salinity change. Decreases in chborophyll per algal cell and in assimilation number were associated with and possibly responsible for some of the decreases in photosynthetic rates. These results show that S. siderea is able to withstand sudden and prolonged, environmentally realistic changes in salinity without measurable whole-animal effects. Further studies are needed to determine whether this species is remarkable in its ability to tolerate salinity change, or whether reef corals are more tolerant to salinity change than is generally believed.