Genomic and single-cell approaches to establish the molecular basis of stony coral resilience to climate change-related stressors.

Project Information

CoralCellSeq

Grant agreement ID: 101065294

DOI

10.3030/101065294

Project closed

EC signature date 15 June 2022

Start date 15 July 2022

End date 14 July 2024

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 181 152,96

Coordinated by

FUNDACIO CENTRE DE REGULACIO GENOMICA
Spain

Periodic Reporting for period 1 - CoralCellSeq (Genomic and single-cell approaches to establish the molecular basis of stony coral resilience to climate change-related stressors.)

Reporting period: 2022-07-15 to 2024-07-14

Summary of the context and overall objectives of the project

The CoralCellSeq project emerges from a pressing global challenge: the alarming degradation of coral reefs due to climate change-induced stressors, such as rising ocean temperatures and acidification. Coral reefs are the foundation of marine biodiversity, offering essential ecosystem services like coastal protection, supporting marine life, and providing economic benefits for millions of people worldwide. However, the rapid increase in ocean temperatures has led to widespread coral bleaching and mortality, threatening the survival of these critical ecosystems. Understanding the cellular and molecular mechanisms behind coral resilience, as well as the symbiosis between corals and algae from the Symbiodiniaceae family, is key to developing effective conservation strategies.
The project focuses on three species of stony corals—Stylophora pistillata, Acropora millepora, and Oculina patagonica—representing both tropical and temperate reef ecosystems. These species exhibit varying levels of resilience to thermal stress, making them ideal models for studying the genetic and cellular factors influencing coral survival. The project leverages advanced genomic and single-cell technologies to create detailed coral cell atlases, providing insights into how coral cells respond to thermal stress and symbiosis dynamics.
The data generated from CoralCellSeq will not only contribute to understanding coral resilience but also position Oculina patagonica, a Mediterranean, temperate, and facultative coral, as a new model organism. Currently, only two single-cell atlases exist for corals—one of which, for Stylophora pistillata, was created by us in a previous study. This comprehensive and in-depth single-cell data will represent the most advanced resource available, offering unparalleled insights into coral biology.
By generating single-cell atlases for each species, CoralCellSeq aims to identify key genes and molecular pathways that play a role in coral resilience. These findings will lay the groundwork for developing future strategies to strengthen coral resilience to environmental changes.
The project's contributions are expected to have a major scientific impact, offering a deeper understanding of coral biology, symbiosis, and resilience. This knowledge will inform future conservation strategies and help mitigate the effects of climate change on coral reefs. The work aligns with global initiatives like the EU Green Deal, supporting biodiversity protection and climate resilience through groundbreaking research on coral ecosystems.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The CoralCellSeq project has focused on understanding coral resilience to climate change stressors by using cutting-edge genomic and single-cell technologies. The main activities and achievements are detailed below.
One of the key accomplishments of the project was generating single-cell atlases for three coral species: Stylophora pistillata, Acropora millepora, and Oculina patagonica. Each atlas represents the most comprehensive dataset currently available for coral biology, covering all known coral cell types, including host cells that bear symbionts. For Stylophora pistillata and Acropora millepora, the project used 10x Genomics technology to FACS-sort and process approximately 40,000 cells per species, of which around 15,000 cells were sequenced. These atlases enabled the identification of 26 distinct cell types in S. pistillata and 27 in A. millepora, providing detailed insights into gene expression profiles at the cellular level. Additionally, an atlas for Oculina patagonica was created, representing a significant breakthrough since this temperate, facultative coral is now positioned as a new model organism for studying coral biology.
In addition to the atlas generation, significant progress was made in identifying genes and pathways involved in coral resilience to thermal stress. The project focused heavily on the gene phd4, which was found to be upregulated in Stylophora pistillata host cells following heat stress. This gene appears to play a role in enhancing resilience to heat, as it was not expressed in the other species studied. These findings have opened new avenues for understanding the molecular mechanisms underlying coral bleaching and survival under elevated temperatures.
The project also included genomic sequencing of Oculina patagonica, resulting in a high-quality, chromosome-level genome assembly. This genome data will greatly facilitate future research into coral resilience and evolution, as well as provide a framework for the study of facultative symbiosis in corals.
In summary, the CoralCellSeq project has made substantial progress in generating critical resources for the coral research community, including single-cell atlases, genome assemblies, and insights into the genetic factors influencing coral resilience. These outputs provide a strong foundation for future conservation strategies aimed at mitigating the effects of climate change on coral reefs.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The CoralCellSeq project has produced several results that push beyond the current state of the art in coral biology and resilience research. One of the most significant advances is the creation of comprehensive single-cell atlases for three species of corals: Stylophora pistillata, Acropora millepora, and Oculina patagonica. Prior to this project, there were only two existing single-cell atlases for corals, with one of them, for Stylophora pistillata, also generated by our team. These new atlases represent the most detailed and extensive cellular datasets for corals available to date, providing unprecedented insights into the gene expression profiles and functional roles of coral cell types, including those involved in symbiosis with algae from the Symbiodiniaceae family.
One of the most groundbreaking aspects of the project is positioning Oculina patagonica, a temperate, facultative coral, as a new model organism. The single-cell atlas and high-quality, chromosome-level genome assembly for this species are the first of their kind, offering a unique opportunity to study facultative symbiosis and the coral’s ability to survive in both symbiotic and aposymbiotic states. This is a significant advancement, as it expands the repertoire of coral models available for studying resilience mechanisms.
Additionally, the discovery of the phd4 gene in Stylophora pistillata, which is highly upregulated in response to heat stress but absent in Acropora millepora and Oculina patagonica, is a key finding. This gene may be central to the mechanisms that allow S. pistillata to withstand elevated temperatures, offering a new target for future research on coral resilience to climate change.
The project has also developed a Shiny app, integrating the single-cell atlases, which will provide the research community with an accessible tool for exploring coral gene expression across different cell types. This platform allows researchers to visualize gene expression patterns, search for specific genes, and generate heat maps, significantly enhancing the ability to explore coral biology at a cellular level.
Overall, CoralCellSeq has not only generated invaluable resources for coral research but has also identified novel genetic pathways involved in coral resilience, providing the foundation for future studies aimed at mitigating coral bleaching and enhancing coral survival in the face of climate change. These achievements set a new benchmark in coral genomics and conservation research.