Coral and Marine Ecosystems Studies

Pervasive tandem duplications and convergent evolution shape coral genomes

The paper reports higher gene counts in two coral genomes due to tandem duplications, suggesting a role in immune system and disease resistance.

Holobiont transcriptomes for the critically endangered staghorn coral (Acropora cervicornis) from two environmentally distinct sites on Turneffe Atoll, Belize

The paper develops transcriptomes for two staghorn coral populations from Turneffe Atoll, Belize, to study gene activity across different taxa in the coral holobiont.

What's left in the tank? Identification of non-ascribed aquarium's coral collections with DNA barcodes as part of an integrated diagnostic approach

This study uses DNA barcoding to identify coral species in aquarium collections, finding that 44% could be identified to species level and 80% provisionally, highlighting biases in reference databases.

Investigating densities of Symbiodiniaceae in two species of Antipatharians (black corals) from Madagascar

The paper investigates Symbiodiniaceae cell density in two black coral species from Madagascar using microscopy and molecular methods, finding low densities and suggesting antipatharians may not rely on high symbiont abundance.

Multi-omics analysis reveals cross-organism interactions in coral holobiont

The paper uses multi-omics data to analyze cross-organism interactions in coral holobionts, revealing host dominance over zooxanthellae and immune responses triggered by Endozoicomonas bacteria.

Metabolomics of healthy and stony coral tissue loss disease affected Montastraea cavernosa corals

The paper uses metabolomics to identify metabolic markers of stony coral tissue loss disease in Montastraea cavernosa, revealing differences between healthy, diseased, and recovered corals.

Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia

The paper investigates mechanisms of ecological divergence with gene flow in corals by combining genomic, transcriptomic, and symbiont analyses to understand adaptation to environmental stress.

Reef Cover: a coral reef classification for global habitat mapping from biophysical remote sensing.

This paper introduces Reef Cover, a coral reef classification system for global habitat mapping using remote sensing data, demonstrating its application in the Pacific Islands.

Physiological and transcriptomic variability indicative of differences in key functions within a single coral colony

The paper examines physiological and transcriptomic differences in a single coral colony, finding distinct functional roles in different polyp locations due to environmental gradients.

Gene expression associated with disease resistance and long-term growth in a reef-building coral

The paper identifies gene expression patterns associated with disease resistance and long-term growth in corals from a marine sanctuary, showing no trade-off between resistance and calcification.

Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

This study presents the Ostreobium nuclear genome and metatranscriptomic analysis to understand its adaptations to the coral skeleton environment and its role in coral holobiont dynamics.

Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata

This study characterizes the thermal stress response in Montipora capitata using transcriptomic and metabolomic data, revealing key gene and metabolite changes associated with stress.

Contraction-expansion dynamics of reef species in response to sea-level changes

The paper addresses the paradox of stable population sizes in reef species despite the contraction-expansion model by proposing a synthetic model of modern reef development and analyzing genetic simulations and molecular evolution rates.

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

The paper identifies genetic adaptations in coral holobionts from the Great Barrier Reef's inshore regions linked to Holocene climate change.

Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events

The paper analyzes transcriptomic responses of Acropora palmata and its symbionts to disease exposure, finding consistent innate immune gene expression despite yearly disease variability.

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

This paper develops a field-friendly framework for characterizing coral holobionts using nanopore sequencing and bioinformatics pipelines, revealing reef-scale bacterial networks and host-specific associations.

Genotypic similarity among algal symbionts corresponds to associations with closely related coral hosts

The paper investigates genetic differentiation of Symbiodinium fitti symbionts associated with three Caribbean coral species and their hybrid, finding host-specific genetic variation.

Identification of novel differentially expressed zooxanthellal genes from Aiptasia-Symbiodinium endosymbiosis through SDS-based RNA purification

The paper identifies differentially expressed zooxanthellal genes in Aiptasia-Symbiodinium endosymbiosis using SDS-based RNA purification and NGS, revealing key cellular processes involved in symbiosis and nonsymbiosis.

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

The paper develops a SNP genotyping array and analysis workflow for Acropora corals and their symbionts, enabling genotype identification and ancestry analysis.

A spatially explicit and mechanistic model for exploring coral reef dynamics

This paper introduces a spatially explicit and mechanistic model to simulate coral reef dynamics, showing that local larval production and growth rate reductions are key factors influencing community dynamics.

The genome sequence of the octocoral Paramuricea clavata - a key resource to study the impact of climate change in the Mediterranean

The paper presents the genome sequence of Paramuricea clavata, a Mediterranean octocoral, to study genetic factors underlying differential responses to thermal stress and support conservation efforts.

Meta-analysis of the General Coral Stress Response: Acropora corals show opposing responses depending on stress intensity

The paper analyzes coral stress responses and finds two distinct types of transcriptional responses to different stress intensities in Acropora corals.

Embryogenesis, polyembryony, and settlement in the gorgonian Plexaura homomalla

This study tracks the development of Plexaura homomalla from eggs to 3-polyp colonies, identifying a novel form of asexual reproduction called polyembryony that may enhance reproductive success in Caribbean octocorals.

Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata

The paper examines genetic structure in Porites lobata corals, finding stronger genetic differentiation across human-impacted habitats than between distant islands.

Convergence of DNA methylation profiles in a novel environment in the reef coral Porites astreoides

This study examines DNA methylation changes in the coral Porites astreoides under simulated environmental change, finding convergence of methylation profiles and evidence of heritability.

Close relationships between coral-associated Chromera strains despite differences within the Symbiodiniaceae

The paper compares transcriptomes of Chromera and Symbiodiniaceae algae to assess their genetic relationships and thermal tolerance.

Light-induced polyp retraction and tissue rupture in the photosensitive, reef-building coral Acropora muricata

The paper develops a light-sheet illumination technique for live imaging of photosensitive corals, revealing light-induced polyp retraction and tissue rupture.

Gene expression of endangered coral (Orbicella spp.) in the Flower Garden Banks National Marine Sanctuary after Hurricane Harvey

This study examines gene expression changes in coral species after Hurricane Harvey, finding oxidative stress responses and sub-lethal stress from poor water quality.

Genome-wide analysis of cell cycle-regulating genes in the symbiotic dinoflagellate Symbiodinium minutum.

The paper identifies cell cycle-regulating genes in Symbiodinium minutum and correlates their expression with cell cycle phases to explore potential control points for algal cell divisions in corals.

The draft genome of the invasive coral Tubastraea sp.

The paper presents the first genome of Tubastraea sp., a fast-spreading invasive coral, and reports its large size, high gene content, and repetitive elements, providing insights into its invasiveness and adaptation.