Research Framework

The genomics research framework was developed to address three key management questions: 

  • How do we preserve the diversity of the ecosystem in the face of climate change?
  • How do we preserve the function of the system in the face of climate change?
  • What innovative approaches could be applied to assist in managing the Reef in the face of climate change? 

The framework

The Sea-quence project delivers the ‘Core enabling infrastructure’. This is the large genomic dataset for 10 critical reef-building corals and their associated microbes and symbionts. This project is the foundation of the research framework.

A dedicated bioinformatics project sits between the core enabling infrastructure project and the five major research themes of the framework. This project will provide the more-specialised bioinformatics required to manage, annotate, analyse, integrate and visualise the framework data to make them accessible to, and optimally useful for, five hypothesis-driven projects.

This genomics data will then underpin 5 major research project themes, which are represented by the 5 coloured boxes within the framework: 

  • Connectivity
  • Stress tolerance
  • Adaptability
  • Role of Microbes
  • Gene function

Project outputs 

These are the potential project outputs under the 5 major research themes.


  • Identify source and sink reefs that would inform spatial planning
  • Predict the likelihood and speed of recovery of a population post disturbance
  • Predict the rate of spread of advantageous mutations and stress-adapted genotypes

Role of Microbes

  • Develop tests to use bacterial communities as indicators of coral health in the face of climate change
  • Understand the role of the coral-algal symbiosis in adaptability to a changing environment


  • Understand the rates and limits of adaptation of key coral and symbiont species and use this information to build better predictive models
  • Identify tolerant coral colonies for use in selective breeding or assisted migration programs

Stress Tolerance

  • Identify genes or markers associated with stress tolerance that could be used in selective breeding programs
  • Develop a biosensor for the early detection of stress in corals

Gene Function

  • Develop coral cell cultures
  • Develop “knock-out” corals for testing gene function

ReFuGe 2020 is a collaboration between

Supported by funding from RioTinto and Bioplatforms Australia and a private family foundation, the Australian Governments's Resilient Coral Reefs Successfully Adapting to Climate Change research and development program and a grant from the Queensland Government Accelerate partnerships fund.