Among the bacteria and archaea there is nothing like the membrane-bound eukaryotic nucleus with its nuclear pore controls of access and egress and the microtubules which control its division by meiosis and mitosis. The eukaryotic nucleus also is able to house two (diploid) or three (triploid) or more (polyploid) sets of chromosomes. These conditions affect the expression of the cell, which is controlled by information in the nucleus.  Everything about the development of the eukaryotic cell is a problem for evolution theory.