The Alpha and Omega of Sigma and Tau; Paleopolyploidy in the Monocots

The structure of the genome ancestral to the Poaceae (Poales) has been controversial, obscured by three rounds (τ, σ and ρ) of whole genome duplication (WGD) since the emergence of the monocots, each WGD followed by a period of fractionation and rearrangement. Pineapple, also in the order Poales, but in the basal bromeliad family, escaped the ρ event. The recent sequencing and annotation of the pineapple genome allowed us a clearer picture of τ and σ so that we could use computational tools to fully resolve the structure of the pre-σ, pre-τ (commelinid) precursor before it radiated into the Arecales, Poales, Zingiberales and other orders. Using as an outgroup the recently sequenced duckweed genome, a monocot that diverged before τ, but that has undergone two successive WGD in its own lineage, we applied the technique of "augmented synteny blocks" to the pineapple genome to clearly establish a seven-chromosome commelinid ancestor. This validates the conclusion of a seven-chromosome ancestor of the cereal family, rather than the five-chromosome or nine-chromosome constructs that also seemed credible based only on sequences within the Poaceae.