Endosymbiotic origin of the Archaeplastida plastid through cyanobacterial primary endosymbiosis. (top) A heterotrophic protist engulfed free-living cyanobacteria for food (phagocytosis). Over time, this situation changed, with the cyanobacterium becoming an endosymbiont (bottom). A chlamydial cell is believed to have also been resident in the host at the time of endosymbiosis and provided functions critical to plastid integration (Ball et al., 2013). Both of these prokaryotes gave rise to nuclear genes in the Archaeplastida host through endosymbiotic gene transfer (EGT; cyanobacterium) and horizontal gene transfer (HGT; chlamydial cell and other bacteria). After their split, the red and green algae gave rise to the plastid in other algae through independent secondary endosymbiosis (Bhattacharya et al., 2004; Curtis et al., 2012). The intracellular transfer of genes via EGT and HGT is indicated (arrows). Genetic material of foreign origin in the nucleus is shown as stripes of different colors with the color indicating the source of the gene.