Working Group
The Plant Evolutionary Genomics working group combines expertise in phylogenetics, developmental biology and informatics to develop improved tools for comparative functional genomics. Gene and genome duplications have played a profound role in plant evolution. Given the high frequency of such duplication events, cross-species comparative analyses of gene expression and function are best considered within the context of gene family phylogenies. A gene family perspective of gene function is required in order to transfer knowledge from experimentally tractable plant species to non-models while accounting for shifts in gene function following duplication events. While phylogenetically grounded comparative studies of gene expression and function have been carried out on a few well studied gene families, methods for ramping up to genome-scale analyses are under development. The working group will advance these efforts by coordinating ongoing development of databases and analysis pipelines that place gene expression and functional data within the context of gene family phylogenies.
The plant evogenomics working group: advancing comparative functional genomics
| PI(s): | Eric Brenner Jim Leebens-Mack (Pennsylvania State University) |
| Start Date: | 1-Mar-2006 |
| End Date: | 29-Feb-2008 |
| Keywords: | phylogenetics, comparative methods, development, genomics, gene structure and function |
The Plant Evolutionary Genomics working group combines expertise in phylogenetics, developmental biology and informatics to develop improved tools for comparative functional genomics. Gene and genome duplications have played a profound role in plant evolution. Given the high frequency of such duplication events, cross-species comparative analyses of gene expression and function are best considered within the context of gene family phylogenies. A gene family perspective of gene function is required in order to transfer knowledge from experimentally tractable plant species to non-models while accounting for shifts in gene function following duplication events. While phylogenetically grounded comparative studies of gene expression and function have been carried out on a few well studied gene families, methods for ramping up to genome-scale analyses are under development. The working group will advance these efforts by coordinating ongoing development of databases and analysis pipelines that place gene expression and functional data within the context of gene family phylogenies.
Related products
Publications- Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Responses to Environmental Stimuli. Plant Physiology Hanada, K., C. Zou, M.D. Lehti-Shiu, K. Shinozaki, and S.H. Shiu (2008). Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Responses to Environmental Stimuli. Plant Physiology 148(2): 993-1003.
- A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms Little, D.P. and D.W. Stevenson (2007). A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 22: 1-21.
- EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes Brenner,E.D., M.S. Katari, D.W. Stevenson, S.A. Rudd, A.W. Douglas, W.N. Moss, R.W. Twigg, S.J. Runko, G.M. Stellari, R.W. McCombie, and G.M. Coruzzi (2005). EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics 6: 143.
- ESTimating plant phylogeny: lessons from partitioning de la Torre, J., M.G. Egan, M. Katari, E.D. Brenner, D.W. Stevenson, G.M. Coruzzi, and R. DeSalle (2006). ESTimating plant phylogeny: lessons from partitioning. BMC Evolutionary Biology 6:48-87.
- Nuclear genome size in Selaginella Little, D.P., R.C. Moran, E.D. Brenner, and D.W. Stevenson (2007). Nuclear genome size in Selaginella. Genome 50: 351-356.
- Mitochondrial data in monocot phylogenetics Petersen, G., O. Seberg, J. Davis, et al. (2006). Mitochondrial data in monocot phylogenetics. Aliso 22: 52-62.
- Phylogeny, genome size, and chromosome evolution of Asparagales Pires, J., I. Maureira, T. Givnish, K. Sytsma, O. Seberg, G. Petersen, J. Davis, D. Stevenson, P. Rudall, M. Fay, and M. Chase (2006). Phylogeny, genome size, and chromosome evolution of Asparagales. Aliso 22: 287-304.
- Taking the first steps towards a standard for reporting in phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA) Leebens-Mack, J., T. Vision, E. Brenner, et al. (2006). Taking the first steps towards a standard for reporting in phylogenies: Minimal Information About a Phylogenetic Analysis (MIAPA). OMICS 10: 231-237.
- Using genomics to study evolutionary origins of seeds Brenner, E. & D. Stevenson. 2006. Using genomics to study evolutionary origins of seeds. Pp. 1- 21 in C. Williams (ed), Landscapes, Genomics, and Transgenic Conifers. Springer-Verlag, Berlin.
