Relevant Group Publications: Genome Res 2003, Trends Genet 2005, Genome Res 2008, Curr Opin Genet Dev 2009.

Via the study of conserved gene order between vertebrate genomes and the phylogenetic analysis of many amphioxus ESTs before the amphioxus genome was sequenced, we provided sufficient evidence supporting the hypothesis claiming the existence of two rounds of whole genome duplication (WGD) during early vertebrate evolution (2R hypothesis) [1,2].

Even with the amphioxus genome present, identifying syntenic segments and estimating genome rearrangement rates in the ancient vertebrate lineages is not trivial as there is no reliable method that could use genomes in scaffold-level assemblies, such as the current amphioxus genome assembly. We developed an own gene pair method to identify syntenic segments which once more illustrated the traces of the vertebrate WGD events. We surprisingly found that, while amphioxus remains the best representative of the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate pre-duplication genome [3].

As opposed to common belief that WGDs induce rearrangements we find that this is not the cause for the duplications at the origin of vertebrates [3]. In fact after reviewing data on WGD events across all three kingdoms of eukaryotic life - including plants, yeast, vertebrates, and human cancers - we find that a variety of outcomes are possible, from genome restructuring to genome stasis. Thus there are no simple rules that can predict a genome's reaction to WGD [4].