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I think weve made surprisingly little progress in understanding diversification events at the origin of eukaryotes. There is currently significant debate as to whether eukaryotes are just another lineage of archaea or whether archaea and eukaryotes constitute distinct groups.

We know also almost very little the origin of the nucleus and the cytoskeleton. It is as if all of a sudden, the eukaryotic lineage emerges with a really complex cytoskeleton and a nucleus, and we really dont know where these structures came from.

Many bacteria do contain homologs of eukaryotic actin (MreB) and tubulin (FtsZ) but if you look across all of the cytoskeleton proteins, there are many that dont have bacterial homologs.