Correction to: Transcriptome of the caribbean stony coral Porites astreoides from three developmental stages.
Ontology highlight
ABSTRACT:
SUBMITTER: Mansour TA
PROVIDER: S-EPMC6857687 | biostudies-literature | 2019 Nov
REPOSITORIES: biostudies-literature
Publications
Correction to: Transcriptome of the caribbean stony coral Porites astreoides from three developmental stages.
Mansour Tamer A TA Rosenthal Joshua J C JJC Brown C Titus CT Roberson Loretta M LM
GigaScience 20191101 11
Similar Datasets
Project description:BackgroundPorites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host-symbiont interactions.FindingsA de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases.ConclusionsThis contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.
| S-EPMC4969664 | biostudies-literature
Project description:In this study, we examine microbial communities of early developmental stages of the coral Porites astreoides by sequence analysis of cloned 16S rRNA genes, terminal restriction fragment length polymorphism (TRFLP), and fluorescence in situ hybridization (FISH) imaging. Bacteria are associated with the ectoderm layer in newly released planula larvae, in 4-day-old planulae, and on the newly forming mesenteries surrounding developing septa in juvenile polyps after settlement. Roseobacter clade-associated (RCA) bacteria and Marinobacter sp. are consistently detected in specimens of P. astreoides spanning three early developmental stages, two locations in the Caribbean and 3 years of collection. Multi-response permutation procedures analysis on the TRFLP results do not support significant variation in the bacterial communities associated with P. astreoides larvae across collection location, collection year or developmental stage. The results are the first evidence of vertical transmission (from parent to offspring) of bacteria in corals. The results also show that at least two groups of bacterial taxa, the RCA bacteria and Marinobacter, are consistently associated with juvenile P. astreoides against a complex background of microbial associations, indicating that some components of the microbial community are long-term associates of the corals and may impact host health and survival.
| S-EPMC3309355 | biostudies-literature
Project description:The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.
| S-EPMC6900098 | biostudies-literature
Project description:To date, most assessments of coral connectivity have emphasized long-distance horizontal dispersal of propagules from one shallow reef to another. The extent of vertical connectivity, however, remains largely understudied. Here, we used newly-developed and existing DNA microsatellite loci for the brooding coral Porites astreoides to assess patterns of horizontal and vertical connectivity in 590 colonies collected from three depth zones (≤10 m, 15-20 m and ≥25 m) at sites in Florida, Bermuda and the U.S. Virgin Islands (USVI). We also tested whether maternal transmission of algal symbionts (Symbiodinium spp.) might limit effective vertical connectivity. Overall, shallow P. astreoides exhibited high gene flow between Florida and USVI, but limited gene flow between these locations and Bermuda. In contrast, there was significant genetic differentiation by depth in Florida (Upper Keys, Lower Keys and Dry Tortugas), but not in Bermuda or USVI, despite strong patterns of depth zonation in algal symbionts at two of these locations. Together, these findings suggest that P. astreoides is effective at dispersing both horizontally and vertically despite its brooding reproductive mode and maternal transmission of algal symbionts. In addition, these findings might help explain the ecological success reported for P. astreoides in the Caribbean in recent decades.
| S-EPMC4761953 | biostudies-literature
Project description:Anthropogenic effects have contributed to substantial declines in coral reefs worldwide. However, some corals are more resilient to environmental changes and have increased in relative abundance, thus these species may shape future reef communities. Here, we provide the first draft reference genome for the mustard hill coral, Porites astreoides, collected in Bermuda. DNA was sequenced via Pacific Biosciences (PacBio) HiFi long-read technology. PacBio read assembly with FALCON UnZip resulted in a 678-Mbp assembly with 3051 contigs with an N50 of 412,256 and the BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An ab initio transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% versus the metazoan gene set. Functional annotation was completed for 86.6% of proteins. These data are valuable resources for improving biological knowledge of P. astreoides, facilitating comparative genomics for corals, and supporting evidence-based restoration and human-assisted evolution of corals.
| S-EPMC9693771 | biostudies-literature
Project description:Mesophotic coral ecosystems between 30-150 m may be important refugia habitat for coral reefs and associated benthic communities from climate change and coastal development. However, reduced light at mesophotic depths may present an energetic challenge to the successful reproduction of light-dependent coral organisms, and limit this refugia potential. Here, the relationship of depth and fecundity was investigated in a brooding depth-generalist scleractinian coral, Porites astreoides from 5-37 m in the U.S. Virgin Islands (USVI) using paraffin tissue histology. Despite a trend of increasing planulae production with depth, no significant differences were found in mean peak planulae density between shallow, mid-depth and mesophotic sites. Differential planulae production over depth is thus controlled by P. astreoides coral cover, which peaks at 10 m and ~35 m in the USVI. These results suggest that mesophotic ecosystems are reproductive refuge for P. astreoides in the USVI, and may behave as refugia for P. astreoides metapopulations providing that vertical larval exchanges are viable.
| S-EPMC4720483 | biostudies-literature
Project description:Apical lesions on Porites astreoides were characterized by the appearance of a thin yellow band, which was preceded by bleaching of the coral tissues and followed by a completely denuded coral skeleton, which often harbored secondary macroalgal colonizers. These characteristics have not been previously described in Porites and do not match common Caribbean coral diseases. The lesions were observed only in warmer months and at shallow depths on the fore reef in Belize. Analysis of the microbial community composition based on the V4 hypervariable region of 16S ribosomal RNA genes revealed that the surface microbiomes associated with nonsymptomatic corals were dominated by the members of the genus Endozoicomonas, consistent with other studies. Comparison of the microbiomes of nonsymptomatic and lesioned coral colonies sampled in July and September revealed two distinct groups, inconsistently related to the disease state of the coral, but showing some temporal signal. The loss of Endozoicomonas was characteristic of lesioned corals, which also harbored potential opportunistic pathogens such as Alternaria, Stenotrophomonas, and Achromobacter. The presence of lesions in P. astreoides coincided with a decrease in the relative abundance of Endozoicomonas, rather than the appearance of specific pathogenic taxa.
| S-EPMC4061089 | biostudies-literature
Project description:With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a ?-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.
| S-EPMC3434190 | biostudies-literature
Project description:A population's potential for rapid evolutionary adaptation can be estimated from the amount of genetic variation in fitness-related traits. Inshore populations of the mustard hill coral (Porites astreoides) have been shown to be more tolerant to thermal stress than offshore populations, but it is unclear whether this difference is due to long-term physiological acclimatization or genetic adaptation. Here, we evaluated variation in growth rate and survival among 38 families of juvenile recruits of P. astreoides spawned by colonies originating from inshore and offshore locations. Recruits were reared in a common garden for 5 weeks and then subjected to two thermal treatments (28 and 31 °C) for 2.5 weeks. The most significant effects were detected during the first 5 weeks, before thermal stress was applied: 27-30% of variance in growth and 94% of variance in recruit survival was attributable to parental effects. Genotyping of eight microsatellite loci indicated that the high early mortality of some of the recruit families was not due to higher inbreeding. Post treatment, parental effects diminished such that only 10-15% of variance in growth rate was explained, which most likely reflects the dissipation of maternal effects. However, offshore-origin recruits still grew significantly less under elevated temperature compared with inshore-origin recruits. These differences observed in naive juvenile corals suggest that population-level variation in fitness in response to different thermal environments has a genetic basis and could represent raw material for natural selection in times of climate change.
| S-EPMC4806898 | biostudies-literature
Project description:Stony Coral Tissue Loss Disease (SCTLD) has caused widespread coral mortality in the Caribbean Region. However, how the disease presence alters the microbiome community, their structure, composition, and metabolic functionality is still poorly understood. In this study, we characterized the microbial communities of the tissues of apparently healthy and diseased SCTLD colonies of the species Siderastrea siderea, Orbicella faveolata, and Montastraea cavernosa to explore putative changes related to the presence of SCTLD. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia were the best represented classes in the healthy tissues of all coral species, and alpha diversity did not show significant differences among the species. The microbial community structure between coral species was significantly different (PERMANOVA: F = 3.46, p = 0.001), and enriched genera were detected for each species: Vibrio and Photobacterium in S. siderea, Spirochaeta2 and Marivivens in O. faveolata and SAR202_clade and Nitrospira in M. cavernosa. Evidence of SCTLD in the microbial communities was more substantial in S. siderea, where differences in alpha diversity, beta diversity, and functional profiles were observed. In O. faveolata, differences were detected only in the community structure, while M. cavernosa samples showed no significant difference. Several microbial groups were found to have enriched abundances in tissue from SCTLD lesions from S. siderea and O. faveolata, but no dominant bacterial group was detected. Our results contribute to understanding microbial diversity associated with three scleractinian coral species and the shifts in their microbiomes associated with SCTLD in the Mexican Caribbean.
| S-EPMC11346732 | biostudies-literature