Abstract
Ancient whole genome duplication (WGD) and the associated processes of chromosomal repatterning, duplicate gene divergence and gene loss have greatly influenced the complexity of life on earth. Genomic data show most angiosperm lineages have at least one WGD in their history. Indentifying evolutionary outcomes of WGDs is integral to understanding plant diversification and function. Comparative analyses of diverse species (i.e. Arabidopsis and grape) or within one family (i.e. grasses) have revealed significant patterns of genomic change after polyploidization. What is lacking are strategic basal-lineage and sister-family comparative analyses allowing for much more precise ancestral genome reconstruction. Inferred ancestral genomes can serve as Rosetta stones to interpret processes of gene retention and loss, origin of novel genes and chromosomal rearrangements. The Brassicaceae is an ideal group for comparative genomics of WGD and ancestral genome reconstruction. First, it contains the premier model Arabidopsis and Brassica crops. Second, there are ten-plus genome projects underway. Third, there is significant synteny across species. Fourth, phylogenetic results support a crown-group radiation, the genus Aethionema as basal and the Cleomaceae as its sister-group. Finally, the crown-group shares the alpha WGD, Aethionema lacks alpha and Cleomaceae has an independent Cs-alpha WGD. I propose to undertake a ?crown-base-sister? comparative analysis including ancestral genome reconstruction. Specifically, I will generate high-density genetic and physical maps for the basal Aethionema arabicum and the sister-lineage Cleome spinosa. The maps will be used as scaffolds for whole genome shotgun sequencing assembly of the ongoing Aethionema and planned Cleome genome projects. This would be the first project to specifically target analysis of WGD associated with a plant family radiation. It will allow me to address fundamental questions about polyploidy, gene retention and chromosomal rearrangements and to translate findings to other lineages.
Netherlands