Embedded Files
Our team offers a strong collaborative and supportive environment with great facilities, infrastructure and network. We emphasize the development of cutting-edge crossover skills between bioinformatics, genetics, and ecology.
If you are interested in joining the team, please get in contact via email.
We are currently seeking domestic and international HDR students, as well as post-doctoral fellows with a background in bioinformatics, molecular biology, biotechnology and/or genetics. Candidates can be supported through Macquarie University HDR and post-doctoral scholarships.
Research background:
Genomics of coral and microalgae
thermal tolerance
Assisted evolution of corals through the lense of AI.
Research background
Coral reefs provide a habitat to ~25% of the species in the marine environment, support the livelihood for ~500 million people on the planet and are of significant economic and cultural value. However, corals have experienced mass bleaching and mass mortalities due to high seawater temperatures caused by climate change. Climate models predict that further warming will continue and mass coral bleaching will become an annual event on most reefs within this century. According to the IUCN, coral reefs are the ecosystems moving most rapidly towards extinction.
For their survival, corals rely on their symbiosis with single celled microalgae. The microalgae provide most of the coral’s nutrition via translocation of photosynthates and also play a crucial part in the thermal tolerance of corals. It is however unclear which genomic adaptations directly contribute to an increased thermal tolerance of the coral and their symbiotic microalgae.
Our projects investigate molecular mechanisms and genomic adaptations that lead to an increased thermal tolerance of corals and their symbiotic microalgae (Symbiodiniaceae). Using molecular techniques, such as genome sequencing, transcriptomics and amplicon sequencing, we analyse adaptations among thermally tolerant and sensitive species. We cultivate the microalgae in the PC2 laboratory at Macquarie University for direct comparisons and experimental assessments of their thermal tolerance capacities.
The outcomes will provide information regarding the molecular mechanisms that can reduce heat stress impacts for corals. Due to the quick deterioration of coral reefs, understanding adaptations that support coral thermal tolerance is a key factor in developing conservation management strategies and associated interventions for reef recovery.
The following research projects are currently available:
Microalgae genomics
Bioinformatics project
This project involves the identification of molecular mechanisms that underpin increased thermal tolerance. The team uses genome and transcriptome sequencing of Symbiodiniacae that have undergone heat-evolution through assisted evolution. We used PacBio Revio long-reads and Hi-C to sequence the genomes of seven close related microalgae (Cladocopium proliferum) that show different thermal tolerances. Our aims are to discover novel single nucleotide polymorphisms, genome rearrangements and overall functional differences between heat-evolved and wild-type algae strains.
Required knowledge: Comfortable with using command line tools in a unix environment and high performance computer.
Collaborators:
Dr Patrick Buerger (Macquarie University)
Dr Amara Jabeen (Macquarie University)
Prof Madeleine van Oppen (Melbourne University)
Dr Cheong Xin Chan (University of Queensland)
Link to further information
Hybrid Coral Genomics
Bioinformatics project
Here, we develop chromosomal-length genomes for 10 coral F1 coral hybrids and determine the recombination events that have occurred in their sperm after meiosis. In this project, we are developing a computational pipeline with existing tools to analyse Hi-C and PacBio Revio data for signatures of molecular mechanisms that promote coral fitness. The aim of the project is to predict thermal tolerance of future hybrid corals through genome sequencing and identification of key genetic signatures.
Required knowledge: Comfortable with using command line tools in a unix environment and high performance computer.
Collaborators:
Dr Patrick Buerger (Macquarie University)
Dr Amara Jabeen (Macquarie University)
Dr Matt Nitschke (Australian Institute of Marine Science)
Prof Madeleine van Oppen (Melbourne University)
Link to further information
Microalgae
SYNTHETIC BIOLOGY
Laboratory based project
Our team works on enhancing the thermal tolerance of Symbiodiniaceae by implementing synthetic biology concepts and genetic engineering techniques targeting both the nucleus and chloroplast. Microalgae form a symbiosis with corals and determine the thermal tolerance of the symbiosis to a large extend. This project is focused on understanding and augmenting the underlying genomic mechanisms of enhanced thermal tolerance in coral associated microalgae.
Required knowledge: Basics of biotechnology laboratory techniques and maintaining sterile working conditions.
Collaborators:
Dr Patrick Buerger (Macquarie University)
Dr Briardo Llorente (ARC Centre of Excellence in Synthetic Biology)
Link to further information
Hybridisation of Symbiodiniaceae
Laboratory based project
This project aims to develop novel phenotypic diversity and genotypes in microalgae through somatic hybridization. The process includes comprehensive physiological and genetic characterisations. We aim to test whether somatic hybridisation can be a tool to enhance thermal tolerance of microalgae. Generating protoplasts of the microalgae will also lead to follow up experiments regarding genetic engineering with different transformation methods to understand their cellular mechanisms.
Required knowledge: Basics of biotechnology laboratory techniques and maintaining sterile working conditions.
Collaborators:
Dr Patrick Buerger (Macquarie University)
Dr Briardo Llorente (ARC Centre of Excellence in Synthetic Biology)
Link to further information
If you are interested in joining the team, please get in contact via email.
We are currently seeking domestic and international HDR students, as well as post-doctoral fellows with a background in bioinformatics, molecular biology, biotechnology and/or genetics. Candidates can be supported through Macquarie University HDR and post-doctoral scholarships.
Google Sites
Report abuse