Overview of phylogeny and fractionated tetraploidies in sequenced eudicot genomes:
Since their divergence, At has had two genome duplication events (known as alpha and beta using the Paterson lab nomenclature, the former being the most recent (Bowers et al., 2003)), Pt has had one genome duplication (, and Cp and Vv have had none. This means that for a single ancestral genomic region, you would expect to find the following derived regions in the extant genomes:
At 4 syntenic regions
Cp 1 syntenic region
Pt 2 syntenic regions
Vv 1 syntenic region
Following genome duplication events, plant genomes undergo massive rearrangements and fractionation (Lockton and Gaut, 2005). Fractionation is the process by which genes are lost from one duplicate genomic region or the other, but not both. Given enough evolutionary time, fractionation will return the gene content of a post-duplicated genome to one more similar to that of the pre-duplicated ancestral genome. However, the local gene content will be different because different genes will be lost from different syntenic regions. Also, since some genes are preferentially retained following genome duplication events (i.e. resistant to fractionation) (Blanc and Wolfe, 2004; Maere et al., 2005; Seoighe and Gehring, 2004; Thomas et al., 2006;), the total gene content of a post-duplicated genome will be different that the pre-duplicated ancestor. These retrained genes are paralogs and homeologs (because they are within the same genome); are also syntelogs (because they are derived from the same ancestral genomic region).
