Evolution is adaptation guided by energy economy. Hence the evolution of eukaryotes was a matter of task division according to relative performance of the different cells involved. A common genetic foundation afforded the necessary chemical communication network. This furthered adaptation geared to efficiency: the least energy expended to produce the desired result.
Over evolutionary time, most of the genes housed in the former bacterial endosymbiont, now mitochondrion-bound, migrated to the genome of the archaeal host. These genes became enclosed in a protective membrane, forming the cell nucleus.
The genes that stayed in the mitochondria were those needed for practicing its core business: coding for proteins which maintain redox balance, which must be synthesized locally to counteract the otherwise deadly effects of ATP-generating electron transport.
In modern eukaryotic cells, the mitochondrial genes resemble those of bacteria, while the original nuclear genome resembles a heritage of bacterial and archaeal origin. Eukaryotic DNA replication descends from archaea, not bacteria.
The acquisition of the mitochondrial power plant gifted eukaryotic cells with 200,000 times the energy available to the average prokaryotic cell. This enabled eukaryotic cells to expand their volume by up to 15,000 times that of the typical bacterium, and to support a genome 5,000 times larger.
After the 1st union of prokaryotes, one or more proto-eukaryote cell types had a 2nd round of endosymbiotic uptake.
Photosynthesis was acquired by endosymbiosis. The ancestor of light-fed algae and progenitor of plants incorporated a cyanobacterium, thus picking up chloroplasts. A chloroplast is the photosynthetic organelle found in algae and plant cells. It is a type of plastid.
Plastids is the catchall term for the major organelles found in the cells of plants and algae. Various plastids have different functions, such as storing starch or fat, or detecting gravity. Some plastids have several internal membrane layers, indicating an independent heritage of endosymbiont incorporation. Algae plastids typically differ from plant plastids.
Like the previous incorporation leading to proto-eukaryotes, many genes of the consumed cyanobacterium that became a chloroplast migrated to the host cell genome. Mechanisms evolved that allowed the proteins encoded by transferred genes to work for the chloroplast colonizer, so as to photosynthesize.
The plastid genome that remained kept its legacy of cyanobacterial origin. But the nuclear genome of plastid-containing eukaryotes is chimeric: containing both the proto-eukaryotic genome and genes derived from the cyanobacterial genome.
The genes to make the enzyme that manufactures the amino acid phenylalanine (Phe) was lifted from an ancient bacterium. Phe is used in many plant products, including lignin, which is critical for the strength of plant cell walls. For animals, Phe is an essential amino acid.
The incorporating evolution of eukaryotes was a milestone, but not as novel as once thought. Some bacteria have protein shell subunits which are functionally equivalent to eukaryotic organelles. Efficiency by division of labor, along with cooperative communication and coordination, existed even in early prokaryotes. There are numerous known examples of cooperative exchange and intimate relationships among prokaryotic microbes.
However impressive in effect, it is only an incremental step from prokaryotic cells aggregating, and sharing genetic material (plasmids), to cooperative envelopment involving different lineages of prokaryotes. Hence, multicellular life was an incremental adaptation from single-celled organisms. In aggregate forms, prokaryotic cells communicate, communally make decisions, and even differentiate; quite like organelles within eukaryotic cells, which communicate and coordinate; as do cells themselves within multicellular organisms.
Larger eukaryotic cells offer efficiencies as well as room for more sophistication. And so more complex organisms are eukaryotic. But there are tradeoffs.
Compared to eukaryotes, smaller size gives prokaryotes a greater surface-area-to-volume ratio, which translates to a higher metabolic rate and a faster growth rate, resulting in shorter generation times. This speed advantage, coupled with horizontal gene transfer, yields a formula for the rapid adaptive capabilities that microbes are known for. Horizontal gene transfer is the environmental depositing and pickup of genic packages which contain actionable intelligence. Bacteria are in the business of being genetic quick-change artists; as are viruses, which carry even less baggage than prokaryotes.