Faculty & Research
- Contact Information
- Contact John Colbourne by jcolbour [at] indiana [dot] edu
- By telephone: 812-856-0099
- By fax: 812-856-9340
- MY 160
- Research Areas
- Genomics and Bioinformatics
Ph.D., University of Guelph, Evolution, 1999.
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 Daphnia pulex genome sequence. Soon, the genome sequence of the distantly related Daphnia 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.
- Wilkes, T., A.C. Darby, J.-H. Choi, J.K. Colbourne, J. H. Werren and G.D.D. Hurst. 2010. The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis. Insect Molecular Biology 19 (Suppl. 1):59-73.
- Darby, A.C. J.-H. Choi, T. Wilkes, M.A. Hughes, J.H. Werren, G.D.D. Hurst and J.K. Colbourne. 2010. Characteristics of the Arsenophonus nasoniae genome; son-killer bacterium of the wasp Nasonia. Insect Molecular Biology 19 (Suppl. 1):75-89.
- Werren, J.H., S. Richards, C.A. Desjardins, O. Niehuis, J. Gadau, J.K. Colbourne (project leaders) et al. 2010. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science: 327:343-348.
- Tang, Z., J.-H. Choi, C. Hemmerich, J.K. Colbourne* and Q. Dong*. 2009. ESTPiper - a web-based analysis pipeline for expressed sequence tags. BMC Genomics 2009, 10:174.
- Meyer, E., G.V. Aglyamova, S. Wang, J. Buchanan-Carter, J.K. Colbourne and M.V. Matz. 2009. Sequencing and de novo analysis of the coral larval transcriptome using 454 FLX. BMC Genomics 2009, 10:219.
- Adamowicz, S.J., A. Petrusek, J.K. Colbourne, P.D.N. Hebert and J.D.S. Witt. 2009. The scale of divergence: a phylogenetic appraisal of intercontinental allopatric speciation in a passively-dispersed zooplankton genus. Molecular Phylogenetics and Evolution 50:423-436.
- Conlon, C., S. McTaggart, J.K. Colbourne, M. Blaxter and T.J. Little. 2009. The components of the Daphnia pulex immune system as revealed by complete genome sequencing. BMC Genomics 2009, 10:175.
- Stillman, J.H., J.K. Colbourne, C.E. Lee, N.H. Patel, M.R. Phillips, D.W. Towle, R.P. Henry, E.A. Johnson, M.E. Pfrender and N.B. Terwilliger. 2008. Recent Advances in Crustacean Genomics. Integrative and Comparative Biology 48:852-868.
- Choi, J-H., S. Kim, H. Tang, J. Andrews, D. Gilbert and J.K. Colbourne. 2008. A machine learning approach to combined evidence validation of genome sequence assemblies. Bioinformatics 24(6):744-750.
- 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. Volume 2:165-219 (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. 2007. 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).
- Yasuhiko, K., K. Kobayashi, S. Oda, J.K. Colbourne, N. Tatarazako, H. Watanabe, T. Iguchi. 2007. Molecular cloning and sexually dimorphic expression of DM-domain genes in Daphnia magna. Genomics 91:94-101.
- 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 8:464.
- 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 8:477.
- 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 100:184-190 (invited paper).