Opportunities
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
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, the understanding of 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. The student will co-develop computational pipelines with existing tools to discover novel single nucleotide polymorphisms, genome rearrangements and overall functional differences between heat-evolved and wild-type algae strains. The candidate will develop skills such as scripting in unix, high performance computing, and statistical comparative analyses in R and other tools.
Required knowledge: Comfortable with using command line tools in a unix environment and high performance computer.
Skills that will be developed: The project focuses on developing skills such as scripting in unix and R, using command line tools on a HPC, statistical comparative analyses, genome assemblies from state-of-the-art sequencing platforms and pipelines, SNP analyses, and general comparative genomics etc. In addition we strongly encourage the development and understanding of a biological and ecological background to complement the bioinformatic analyses.
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 student will integrate into the team and contribute with their analyses to data mining. 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.
Skills that will be developed: The project focuses on developing skills such as scripting in unix and R, using command line tools on a HPC, statistical comparative analyses, genome assemblies from state-of-the-art sequencing platforms and pipelines, SNP analyses, and general comparative genomics etc. In addition we strongly encourage the development and understanding of a biological and ecological background to complement the bioinformatic analyses.
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 genetic engineering
Laboratory based project
Our team works on enhancing the thermal tolerance of Symbiodiniaceae by implementing 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 genetic engineering to understand the underlying genomic mechanisms of enhanced thermal tolerance in coral associated microalgae. The candidate will develop skills to build genetic constructs for the target species and use biolistics to genetically transform microalgae, starting with fluorescence dyes to distinguish transient from non-transient cells and antibiotic resistance trials. The aim of the project is to establish an assay to genetically transform the nuclear genome of symbiotic microalgae.
Required knowledge: Basics of biotechnology laboratory techniques and maintaining sterile working conditions.
Skills that will be developed: The project focuses on developing biotechnology skills such as transforming microalgae, genetic construct design and genomic characterisations. This will create a strong foundation in biotechnology laboratory techniques and profound understanding of genomics.
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. The student will learn laboratory techniques of microalgae culturing, generating protoplasts from microalgae cultures, somatic hybridisation and physiological characterisation of the target species. 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.
Skills that will be developed: The project focuses on developing biotechnology skills, such as the generation of protoplasts for somatic hybridisation, genomic characterisations and microalgae culturing. This will create a strong foundation in biotechnology laboratory techniques and profound understanding of genomics.
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.