An interesting pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D or A) along with one or two differential subgenomes which is modified relative to other diploid and allopolyploid species containing this genome(s). This status that has been referred to as oepivotaldifferential genome evolution was first identified based on comparative morphology (flowering spikes), whereby species could be grouped into A, D and U genome clusters. However, substantial cytogenetic evidence also supports this genome relationship, and with recent genomic advancements in wheat we suggest that it is time to interrogate this relationship further, and to extend these concepts to other plant taxa where it may be relevant. The pivotal-differential genome patterning within taxa may have three possible explanations that should be tested. Firstly, variation between species sharing a differential genome may be directly inherited from variation (e.g. different progenitor cytotypes or subspecies) present within the ancestral diploid species. Secondly, variation between species may be induced as a result of the allopolyploidy followed by the dominance of one subgenome over the other(s). Thirdly, hybridization between two allopolyploid species that share a (pivotal) genome in common but differ in their second genome may give rise to a new, rearranged (differential) genome after hybridization and genome stabilization (e.g. AABB x AACC -> AADD). Interrogation of future pan-genome data coupledwith synthetic recreation of historical hybridization events can reveal the mechanisms underlying pivotal-differential genome patterns.
