Gene family and genome evolution
From Shiu Lab
One of the major mechanisms for generating duplicate genes is by whole genome duplication (polyploidization). In plants, this process occurs frequently and includes doubling of the same genome (autopolyploidy) or hybridization of different species (allopolyploidy). As a result, it is common to find polyploids in the vicinity of their diploid ancestors. This offers an excellent opportunity for monitoring gene losses in natural and synthetic polyploid populations. Specifically, we are looking into the gene losses in a recently created allotetraploid Arabidopsis suecica and its putative progenitors. We investigate the genome changes in the polyploids using the tiling array, a high density array of the Arabidopsis thaliana genome with 35bp resolution. The outcomes will provide clues on the rate of gene losses and information on the genes that preferentially retained in the early history of polyploid evolution. In addition to monitoring the genome dynamics of polyploids, we analyze the available eukaryote genomes via computational approaches to evaluate the long-term trend of gene gains and losses and the evolutionary history of all gene families in various eukaryotes.
