Postdoctoral Fellow
Availability of genomic sequences from a wide variety of taxa are revealing intriguing patterns in genomic evolution, including gene content and chromosomal structure. One of the most striking and variable contrasts between genomes arises when comparing the repetitive element compliment of genomes. A large proportion of eukaryotic genomes is comprised of widely variable but repetitive centromeric, telomeric, and transposable elements (TEs). Evidence from several evolutionary lineages suggests TEs contribute to changes in genome structure and function by altering genome size, gene expression and the rate and placement of recombination. These genomic changes, in turn, result in corresponding changes to morphology and life history traits. Despite the prevalence and importance of TEs to organismal and genomic evolution, research that compares patterns of TE proliferation between organisms is still in its infancy. I propose to explore TE presence and distribution in a phylogenetic framework in the Asparagales (onion, asparagus, iris, agave, orchid), a diverse order of plants about which little genomic information is published, but which contains enormous variation in both genome size and life history traits. First, I plan to mine genome sequence surveys from across Asparagales to characterize and quantify TEs within an organism. Second, I will develop a qualitative framework with which to compare proliferation of TEs using a phylogeny. Finally, I plan to explore possible correlations between TE proliferation, diversification rates and life history traits.
Comparative biology of transposable element proliferation
| PI(s): | Kate Hertweck |
| Start Date: | 1-Sep-2011 |
| End Date: | 1-Dec-2014 |
| Keywords: | evolutionary genetics, genomics, phylogenetics, selfish genes, comparative methods |
Availability of genomic sequences from a wide variety of taxa are revealing intriguing patterns in genomic evolution, including gene content and chromosomal structure. One of the most striking and variable contrasts between genomes arises when comparing the repetitive element compliment of genomes. A large proportion of eukaryotic genomes is comprised of widely variable but repetitive centromeric, telomeric, and transposable elements (TEs). Evidence from several evolutionary lineages suggests TEs contribute to changes in genome structure and function by altering genome size, gene expression and the rate and placement of recombination. These genomic changes, in turn, result in corresponding changes to morphology and life history traits. Despite the prevalence and importance of TEs to organismal and genomic evolution, research that compares patterns of TE proliferation between organisms is still in its infancy. I propose to explore TE presence and distribution in a phylogenetic framework in the Asparagales (onion, asparagus, iris, agave, orchid), a diverse order of plants about which little genomic information is published, but which contains enormous variation in both genome size and life history traits. First, I plan to mine genome sequence surveys from across Asparagales to characterize and quantify TEs within an organism. Second, I will develop a qualitative framework with which to compare proliferation of TEs using a phylogeny. Finally, I plan to explore possible correlations between TE proliferation, diversification rates and life history traits. Related products
Software and Datasets- Hertweck KL (2013) Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Dryad Digital Repository. doi:10.5061/dryad.43g64
- Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Hertweck, K. (2013). Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Genome, (ja).
- Hertweck, K. L. and M. McKain. Estimation of divergence times in Asparagales in the presence of hybridization. Invited talk in the Paleobotany Symposium at Monocots V: 5th International Conference on Comparative Biology of Monocotyledons.
- Hertweck, K. L., M. A., Han, J. L., Phillips, Greer, L. F., Graves, M., Rose, M. R. 2013. Genome-wide transposable element insertion frequencies change with selection for accelerated development. Evolution, Snow Bird, Utah.
- Hertweck, K. L. 2013. Transposable element proliferation and genome size evolution in Asparagales. Poster at Plant Animal Genome (PAG) XXI Meeting, San Diego, CA
- Hertweck, K. L. and J. C. Pires. 2012. Assembly of repetitive DNA from genome survey sequencing: Lessons from grasses and applications to non-model systems. Evolution, Ottawa, Ontario, Canada.
- Hertweck, K. L. 2012. From environmental adaptation in plants to human disease: The widespread genomic effects of junk DNA. Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) National Meeting, Seattle, Washington.
- Hertweck, K. L. 2012. Genome-wide effects of transposable element evolution. Invited seminar at University of Virginia Ecology and Evolutionary Biology Department.
