Mail Address: Comparative Genomics Centre,
Molecular Sciences Bldg 21, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 6923 Fax:  61-7-4781 6078


Research Overview
Research Projects
Recent Publications
Recent Press Coverage
Student Supervisions
Available projects


        The success of coral reefs is dependent upon the symbiosis between scleractinian (reef building) corals and a unicellular dinoflagellate of the genus Symbiodinium (also called zooxanthellae) that lives within the coral tissue. These photosynthetic zooxanthellae provide the majority of the energy that the coral host requires to live, grow, reproduce and generate the calcium carbonate reef. However, in addition to being key to the survival of reefs they may also be the weak link in the survival of coral reefs in the future. Coral reefs are the world are currently threatened by a variety of anthropogenic stressors such as global warming, increasing CO2 concentrations and eutrophication, and it is often the zooxanthellae that are the most susceptible to these stress events. Despite their importance, not only to corals but also in the general phytoplankton community, we know very little of their genomes.

        Dinoflagellates as a group have a unique genetic heritage; they have very large genomes (often larger than that of humans), only about half of them are photosynthetic, their chromosomes remain permanently condensed, they are the only known eukaryote known to utilise 5-hydroxymethyluracil and their chloroplast genomes have been greatly reduced. Despite these novel characteristics it is only recently that various groups have begun to examine the genetic compliment of dinoflagellates.

        The study organism of choice for the Symbiosis Genomics group is the dinoflagellate Symbiodinium. The Symbiosis Genomics group focuses on linking changes in the gene expression of Symbiodinium to physiological of the algae and the intact coral holobiont (its host), and subsequent ecological changes. Research of this type can broadly be called ecological genomics. In particular we are interested in how these dinoflagellates respond to human induced stress, such as climate change, what effects these changes have on the coral host and how these responses of the alga effect the future of coral reefs as we know them.


1. Characterising the Symbiodinium transcriptome
        One of the major research efforts in the group is to explore the transcriptome of Symbiodinium, without a knowledge of which genes are present in an organism it is impossible, in particular we are interested in genes that are expressed in response to stress (see Leggat et al. 2007). We have now sequences over 6000 expressed sequences tags (ESTs) which encode approximately 4000 different genes. Further sequencing efforts are continuing as we are still finding a new and novel genes as we sequence more clones. This research has thrown up a number of novel findings (see Weird “Engine of the Reef” Revealed) which have changed the way in which we look at these unique algae. Currently more than half of the genes that we have found are of unknown function, indicating how little we know about these important organisms. We are now comparing our analysis with other EST projects performed on Symbiodinium from the Caribbean to determine if there are significant differences between the alga from the Great Barrier Reef and those in the Caribbean.
2. Symbiodinium microarrays
        This group (with other collaborators) have developed the first cDNA microarray for Symbiodinium (clade C3). Use of these arrays provide a key platform for the study of the Symbiodinium and is important in studies examining how Symbiodinium respond to stress and also how different strains behave.

3. The response of Symbiodinium to stress- are they a weak link in the coral symbiosis?
        There is a range of evidence that indicates that in the coral-algal symbiosis it is Symbiodinium which hare the weak link. We are examining how both the algae and coral respond to stress, in particular those caused by humans such as global warming, increasing CO2 levels and eutrophication. This research effort is aimed to determine how the alga (and subsequently the intact association) responds to stress by linking changes in the expression of key genes to physiological responses. In addition we are taking a broad scale approach by utilising microarray technology. This group (with collaborators) have developed the first cDNA microarrays for Symbiodinium which will allow for the use of the cutting edge technology coupled with more traditional physiological and field based studies.

4. Ecotypes of Symbiodinium
        Although generically called Symbiodinium this genus contains huge diversity (which might be equivalent to that found in other orders of dinoflagellates), to date there are eight different “clades” (A-H) that have been characterised using molecular techniques. Within each clade there are numerous subclades. A variety of studies have shown that there are recognisable patterns of distribution of Symbiodinium (at both the cladal and subcladal level) between different hosts and across environmental gradients. Some Symbiodinium can be considered to be generalists while others are specialists, yet despite this we still do not know what the functional differences between the different Symbiodinium types are. This work is utilising the concept of an “ecotype” is characterising the sequence difference, gene expression differences and physiological differences of various Symbiodinium strains under different conditions. This information will determine the ecological relevance of different Symbiodinium strains to the intact coral-algal holobiont.


Group Head
Graduate Students
Honour Students


Students interested in undertaking a PhD or Masters project in the Symbiosis Genomics Group should contact Bill Leggat to discuss projects of mutual interest. Most higher degrees students would be expected to be eligible for a scholarship through the Australian Postgraduate Award (APA) scheme, the James Cook University Postgraduate Research Scholarship or an equivalent national or international scholarship.

The Australian Postgraduate Award (APA) and James Cook University Postgraduate Research Scholarship (JCUPRS) are open to applicants with, or who expect to hold, a first class honours degree or equivalent by the end of the year and who wish to undertake full-time research Masters or PhD program. In 2010 the stipends for an APA were $22,500 pa (full time) or $12,176 (part-time). APA applicants must be Australian citizens or have been granted permanent resident status and lived in Australia continuously for 12 months prior to receiving the award; Information and application forms can be obtained from the Graduate Research School.  Closing Date: 31 October of each year.

Students who have completed their undergraduate training in a BSc, BBiomedSc, BMedlabSc or equivalent program and are interested in participating in the Biochemistry and Molecular Biology Honours Program are encouraged to contact Bill Leggat for a description of currently available projects. Honours studies require a full-time commitment for one year (two semesters) and can start in either February or August.

There are two main opportunities for undergraduates to participate in the ongoing research of the Symbiosis Genomics Group.

Students enrolled in BC3203 (Special Topics in Biochemistry and Molecular Biology - second semester) could ask that they undertake their research project in the Symbiosis Genomics Laboratory.

Students can apply for a Comparative Genomics Centre Vacation Scholar Award. The successful applicants receive instruction in the latest recombinant DNA and genetics techniques, receiving a stipend of $200 per week for a full-time commitment of between 6 and 10 weeks over the summer break. Applications for the CGC Vacation Studentships are announced in September each year and close in late October. Contact Bill Leggat for further details



1.    National Geographic News – Moonlight triggers mass coral “romance”.
2.    Science Daily – Weird “Engine of the Reef” Revealed.
3.    Science Magazine - REEFS IN TROUBLE: Moonlight Sonata on the Reef



1.    Lynda Boldt - Symbiodinium light regulated genes and the affect of varying environmental stresses
2.    Teressa Bobeszko 
– The role of carbonic anhydrase in the coral-dinoflagellate symbiosis
3.    Brent Knack
– Characterisation of integrin subunits in Acropora millepora
4.    Annamieke van den Heuvel
- Characterization of genes, proteins and the regulatory pathways involved in nitrogen uptake and assimilation in Acropora aspera and its symbiont Symbiodinium sp.
5.    Jeffry Deckenback
Maturation, turn-over, oligomerization, and transport of pocilloporins
6.    Charlotte Kvennefors 
Host-pathogen interactions in reef building corals
7.    Ruth Reef
- The effect of temperature on the accumulation and repair of UV damage in zooxanthellae and corals and its ecological significance


1.    Tamsyn Garby – The role of metacaspases in Symbiodinium cell death

Honours Students

1.    Teressa Bobeszko (2007)– Honours 1A
2.    Rachael Middlebrook (2006) – Honours 1A
3.    Lynda Boldt (2005) – Honours 1A
4.    Annamieke van den Heuvel (2005) – Honours 1A
5.    Alick Lau (2003)– Honours 2A


Autoimmunity Research Group, Medical Genomics Rseearch Group, James Cook University, Key words: Immunology, immune, immunogenetics, disease, risk, vaccine, Genetics, Genomics, Phenomics, Proteinomics, Gene, Autoimmune diabetes, Type 1 diabetes mellitus, childhood diabetes, lupus, systemic lupus erythematosus, haemolytic anaemia, hemolytic anemia, Coombs' test, antinuclear antibodies, renal failure, glomerulonephritis, gastritis, type A gastritis, pernicious anemia, immunology, popular science, biology.