Associate Scientist
Genomics Director, The Center for Genomics and Bioinformatics

Phone: 812/856-0099
Fax: 812/855-6082
Email John

Daphnia Genomics Consortium

Studies in my lab encompass the fields of evolutionary ecology, molecular biology, systematics, and functional genomics. From this blend of disciplines emerges a research program that centers on connecting gene expression and genome structure with individual fitness and population-level responses to environmental challenges. However, few animal models amendable to genomics research today have equally compelling ecological attributes to effectively integrate ecology and evolution with functional genomics. For instance, species like Drosophila (fly) and Caenorhabditis (nematode worm) are gainfully used to decode the complex genetic mechanisms that underlie cellular and developmental processes, but these animals provide only limited opportunities to extend genomic studies to variation within natural populations.

It is therefore the long term research goal of my group to develop Daphnia into a new model organism to study (i) the functional mechanisms of phenotypic plasticity - including environmental sex determination and cyclomorphosis - (ii) the genetic basis of evolutionary adaptation within natural populations, and (iii) the physiological and evolutionary potential of aquatic organisms to counter chemical threats (pollution) in the environment. This aquatic crustacean has been a focus of ecological studies for over 200 years. As a result, its ecology and evolutionary history are superbly understood. Most recently, Daphnia emerges as one of the best characterized genomic systems, primarily because of work that we do in conjunction with the Daphnia Genomics Consortium and the Joint Genome Institute for having completed the draft assembly and annotation of the D. pulex genome sequence. Soon, the genome sequence of the distantly related D. magna (used to set regulatory limits by environmental protection agencies) will also be in hand.

Finally, recognizing the importance of the first crustacean genome sequence, which appropriately roots the phylogeny of insect model systems for the study of molecular genetics and development, the expertise of my lab includes a growing number of other arthropod genomics projects (including flies, ticks, wasp, scuds) for the planning stages of an Arthropod Comparative Genomics Initiative.

Shaw, J.R., J.K Colbourne, J.C. Davey, S.P. Glaholt, T.H. Hampton, Y. Chen, L. Folt, J.W. Hamilton. 2007. Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveal a novel crustacean metallothionein. BMC Genomics. In revision.

Shaw, J.R., M. Pfrender, B.D. Eads, R. Klaper, A. Callaghan, I. Colson, B. Jansen, D. Gilbert and J.K. Colbourne. 2007. Daphnia as an emerging model for toxicological genomics. In: Advances in experimental biology on toxicogenomics. eds. C. Hogstrand and P. Kille. Elsevier Press. In Press.

Eads, B.D., J.K. Colbourne, E. Bohuski and J. Andrews. 2007. Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex. BMC Genomics, In revision.

Colbourne, J.K., B.D. Eads, J. Shaw, E. Bohuski, D. Bauer and J. Andrews. 2007. Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes. BMC Genomics 8:217.

Eads, B.D., J. Andrews and J.K. Colbourne. 2007. Ecological genomics in Daphnia: stress responses and environmental sex determination. Heredity (23 May 2007) (invited paper).

Denslow, N.D., J.K. Colbourne, D. Dix, J. Freedman, C. Helbing, S. Kennedy and P. Williams. Selection of surrogate animal species for comparative toxicogenomics. 2006. In: Emerging Molecular and Computational Approaches for Cross-Species Extrapolations. eds. W.H. Benson and R.T. Di Giulio. CRC Press. pp. 33-75. (invited paper).

Cristescu, M.E.A., J.K. Colbourne, J. Radivojac, M. Lynch. 2006. A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics. Genomics 88:415-430.

Colbourne, J.K., C.C. Wilson and P.D.N. Hebert. 2006. The systematics of Australian Daphnia and Daphniopsis (Crustacea: Cladocera): a shared phylogenetic history transformed by habitat specific rates of evolution. Biological Journal of the Linnean Society 83:469-488.

Paland, S., J.K. Colbourne and M. Lynch. 2005. Evolutionary history of contagious asexuality in Daphnia pulex. Evolution 59:800-813.

Colbourne, J.K., V.R. Singan and D. Gilbert. 2005. wFleaBase: the Daphnia genome database. BMC Bioinformatics 6:45.

Stewart, C.A., R. Keller, R. Repaski, M. Hess, D. Hart, M. Mller, R. Sheppard, U. Wssner, J.K. Colbourne, M. Aumller, H. Li and D.K. Berry. 2004. A global grid for analysis of arthropod evolution. Proceedings of the Fifth IEEE/ACM International Workshop on Grid Computing 1550-5510/04.

Colbourne, J.K., B. Robison, K. Bogart and M. Lynch. 2004. Five hundred and twenty eight microsatellite markers for ecological genomic investigations using Daphnia. Molecular Ecology Notes 4:485-490.