CORAL GENOMICS GROUP
COMPARATIVE GENOMICS CENTRE

Mail Address: Comparative Genomics Centre,
Molecular Sciences Bldg 21, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 6265 Fax:  61-7-4781 6078


 CONTENTS:

RESEARCH OVERVIEW:
 
 
 
    Our understanding of metazoan genome evolution is based on a small number of complete genome sequences and large EST (Express Sequence Tags) datasets that represent only a few complex animals. Of necessity, therefore, deductions about the evolutionary origins and structures of human genes are largely based on comparisons with the genomes of the insects Drosophila melanogaster and Anopheles gambiae, the nematode Caenorhabditis elegans and the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The study of the evolution of developmental genes has identified some spectacular examples of conservation of developmental programs, particularly between D. melanogaster and vertebrates. However, a significant number of D. melanogaster and C. elegans genes are highly modified, and the extent of gene loss in these organisms is unknown. Substantial differences between the D. melanogaster and C. elegans genomes, together with the fact that the nematodes and arthropods are now regarded as more closely related than was previously the case, imply that comparisons based only on these organisms may give a misleading view of the ancestral metazoan.

  In terms of understanding the evolution of metazoan genetic and developmental complexity, the Cnidaria are likely to be critically important, as this phylum is regarded as the sister group to the Bilateria. For these reasons, we are using a local cnidarian, the reef-building coral Acropora, as a model system in order to investigate several issues central to the evolution of developmental mechanisms.  Over the last few years, we have established most of the standard molecular methods (in situ hybridisation technology etc.) and tools (genetic libraries etc.) for Acropora, and this has lead to increasing recognition of its value as a comparator by the international community. At present we are using Acropora to address several questions that are central to nervous system development and the evolution of developmental mechanisms.
Anthozoan cnidarians such as Acropora possess the most 'primitive' present-day nervous systems, a morphologically homogeneous nerve net. However, an ongoing EST project that we are carrying out has identified a large number of genes involved in specifying and patterning the advanced nervous systems of flies and mammals. We have shown that several of these genes are expressed in the coral in patterns that resemble those seen in vertebrates. In addition, the cnidarian nervous system appears to be entirely dispensable, as it is possible to indefinitely culture hydra after destroying all nerve cells and the interstitial cells that give rise to them. Therefore despite its apparent simplicity, plasticity and regenerative capabilities, the cnidarian nervous system is patterned by genes related to those of vertebrates. Cnidarians are therefore potentially highly informative for many aspects of nervous system specification and regeneration.
 

 

Evolutionary Genetics
We use Acropora as a model for understanding the evolutionary processes affecting sessile marine invertebrates in general, as these appear to evolve in very different ways to the terrestrial animals upon which much of our understanding of evolutionary processes is based. One of the major differences between these systems is that many sessile marine invertebrates release their gametes into the water column where fertilization takes place. This creates unparalleled opportunities for interspecific hybridization and introgression between species, as has been documented for many species of reef corals. Molecular data and experimental breeding trials have confirmed that interspecific hybridisation occurs and is likely to have contributed to the evolution of modern Indo-Pacific coral species including the genus Acropora
 
    Acropora is the largest extant reef-building coral genus, and is also one of the world’s most widespread scleractinian coral genera, spanning the Indian and Pacific Oceans and the Caribbean Sea. Some species have very restricted distributions, whereas others are found throughout large parts of the tropics, and up to 70 Acropora species can be found in sympatry. An enormous amount of intraspecific morphological variability exists, while at the same time similarities between species are striking; for example, intraspecific geographic differences in morphology can be as large as differences between species. Acropora thus provides an ideal model system for examining speciation and evolution of scleractinian reef coral species in general, on both temporal and spatial scale.
   Whilst interspecific hybridisation clearly occurs between coral species, population genetic approaches indicate that it occurs with much lower frequency than would be expected on the basis of in vitro breeding trials. This implies the existence of (imperfect) gamete recognition systems in corals. A particular area of interest to us is therefore to unravel the basis of coral gamete specificity. Some candidate molecules have emerged from the EST project, and we are presently investigating these.

Coral Spawning
Coral spawning is an intense period of activity for us as, over a period of a few days each year, we try to collect and preserve sufficient embryonic and larval coral material to sustain lab activities for the rest of the year. We also carry out many experiments on the reproductive and developmental biology of Acropora at that time. Fieldwork during coral spawning is generally carried out from Magnetic sland, and takes place following the full moon in mid-late October. The fact that the main reefs generally spawn one lunar month after inshore reefs (such as those around Magnetic Island enables us also to collect material from the University’s research station on Orpheus Island if we need to. We have also carried out fieldwork on the West Australian reefs, which spawn during autumn rather than spring

Dinoflagellate Genetics
All reef-building corals form obligate symbioses with unicellular algae belonging to the dinoflagellate genus Symbiodinium (nominally a single genus but actually a highly diverse group of organisms) ­ the ability of corals to calcify at rates required to build reefs requires high levels of photosynthesis in their algal symbionts. We are interested in both basic and evolutionary genetics of dinoflagellate. Dinoflagellates are unique eukaryotes in many ways ­ for example, components of their light-harvesting complexes are unrelated to any known proteins, and they do not contain true histone proteins. Little is known about the molecular basis of the interaction of the algae with their coral hosts, nor about the specificity of the interaction.

STAFF
Group Head: Research Staff


Graduate Students




POSITIONS IN THE CORAL GENOMICS GROUP:

Postgraduate
Students interested in undertaking a PhD or Masters project in the Coral Genomics Group should contact David Miller 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.

Honours
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 David Miller 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. Follow this link for details.

Undergraduate
There are two main opportunities for undergraduates to participate in the ongoing research of the Coral 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 Coral Genomics Laboratory.

Students can apply for a Comparative Genomics Centre Vacation Scholar Award. The successful applicants receive instruction in the latest genetic and immunological 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 David Miller for further details.

PUBLICATIONS:

Forêt, Sylvain, Seneca, François, De Jong, Danielle, Bieller, Annette, Hemmrich, Georg, Augustin, Rene, Hayward, David C., Ball, Eldon E., Bosch, Thomas C.G., Agata, Kiyokazu, Hassel, Monika, and Miller, David J. (2011) Phylogenomics reveals an anomalous distribution of USP genes in metazoans. Molecular Biology and Evolution, 28 (1). pp. 153-161. ISSN 1537-1719

Kitahara, Marcelo V., Cairns, Stephen D., Stolarski, Jaroslaw, Blair, David, and Miller, David J. (2010) A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS ONE, 5 (7). pp. 1-9. ISSN 1932-6203

Ball, Eldon E., and Miller, David J. (2010) Putting placozoans on the (phylogeographic) map. Molecular Ecology, 19 (11). pp. 2181-2183. ISSN 1365-294X

Hartmann, Beata, Müller, Michael, Hislop, Nikki R., Roth , Bettina, Tomljenovic, Lucija, Miller, David J., and Reichert, Heinrich (2010) Coral emx-Am can substitute for Drosophila empty spiracles function in head, but not brain development. Developmental Biology, 340 (1). pp. 125-133. ISSN 1095-564X

Forêt, Sylvain, Knack, Brent, Houliston, Evelyn, Momose, Tsuyoshi, Manuel, Michael, Quéinnec, Eric, Hayward, David C., Ball, Eldon E., and Miller, David J. (2010) New tricks with old genes: the genetic bases of novel cnidarian traits. Trends in Genetics, 26 (4). pp. 154-158. ISSN 1362-4555

Kitahara, Marcelo V., Cairns, Stephen D., and Miller, David J. (2010) Monophyletic origin of Caryophyllia (Scleractinia, Caryophylliidae), with descriptions of six new species. Systematics and Biodiversity, 8 (1). pp. 91-118. ISSN 1478-0933

Miller, David J., and Technau, Ulrich (2010) Understanding the evolution of multicellularity; insights from basal metazoans. BioEssays, 32 (2). pp. 175-178. ISSN 1521-1878

Richards, Zoe T., Wallace, Carden C., and Miller, David J. (2010) Archetypal elkhorn coral discovered in the Pacific Ocean. Systematics and Biodiversity, 8 (2). pp. 281-288. ISSN 1478-0933

Seneca, Francois O., Forêt , Sylvain, Ball, Eldon E., Smith-Keune, Carolyn, Miller, David J., and van Oppen, Madeleine J.H. (2010) Patterns of gene expression in a scleractinian coral undergoing natural bleaching. Marine Biotechnology, 12 (5). pp. 594-604. ISSN 1436-2236

Reyes-Bermudez, A., and Miller, D.J. (2009) In vitro culture of cells derived from larvae of the staghorn coral Acropora millepora. Coral Reefs, 28 (4). pp. 859-864. ISSN 1432-0975

Zhou, Yan, et al  (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature, 460 . pp. 345-352. ISSN 1476-4687

Bay, Line K., Ulstrup, Karin E., Nielsen, H. Bjorn, Jarmer, Hanne, Goffard, Nicolas, Willis, Bette L., Miller, David J., and van Oppen, Madeleine J.H. (2009) Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora. Molecular Ecology, 18 (14). pp. 3062-3075. ISSN 1365-294X

Reyes-Bermudez, Alejandro, Lin, Zhiyi, Hayward, David C., Miller, David J., and Ball, Eldon E. (2009) Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora. BMC Evolutionary Biology, 9 (178). - . ISSN 1471-2148

Iguchi, Akira, Morita, Masaya, Nakajima, Yuichi, Nishikawa, Akira, and Miller, David (2009) In vitro fertilization efficiency in Acropora digitifera. Zygote, 17 . pp. 225-227. ISSN 1469-8730

Shinzato, Chuya, Iguchi, Akira, Hayward, David C., Technau, Ulrich, Ball, Eldon B., and Miller, David J. (2008) Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa. BMC Evolutionary Biology, 8 . . ISSN 1471-2148

Miller, David J., and Ball, Eldon B. (2008) Animal evolution: Trichoplax, trees and taxonomic turmoil. Current Biology, 18 (21). pp. 1003-1005. ISSN 1879-0445

Knack, Brent A., Iguchi, Akira, Shinzato, Chuya, Hayward, David C., Ball, Eldon B., and Miller, David J. (2008) Unexpected diversity of cnidarian integrins: expression during coral gastrulation. BMC Evolutionary Biology, 8 . - . ISSN 1471-2148

Miller, David J., and Ball, Eldon E. (2008) Cryptic complexity captured: the Nematostellar genome reveals its secrets. Trends in Genetics, 24 (1). pp. 1-4. ISSN 1362-4555

Alieva, Naila O., Konzen, Karen A., Field, Steven F., Meleshkevitch, Ella A., Hunt, Marguerite E., Beltran Ramirez, Victor, Miller, David J., Wiedenmann, Jorg, Salih, Anya, and Matz, Mikhail V. (2008) Diversity and evolution of coral fluorescent proteins. Public Library of Science ONE , 3 (7). pp. 1-12. ISSN 1932-6203

Grasso, Loretta C., Maindonald, John, Rudd, Stephen, Hayward, David C., Saint, Robert, Miller, David J., and Ball, Eldon E. (2008) Microarray analysis identifies candidate genes for key roles in coral development. BMC Genomics, 9 . pp. 540-557. ISSN 1471-2164

Richards, Zoe T., van Oppen, Madeleine J.H., Wallace, Carden C., Willis, Bette L., and Miller, David J. (2008) Some rare Indo-Pacific coral species are probable hybrids. Public Library of Science ONE , 3 (9). pp. 1-8. ISSN 1932-6203


 

LINKS:
 

 

Comparative Genomics Centre, Center, James Cook University, Key words: Coral, Genetics, gene, genome, DNA, linkage, 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.