Fig. 5

Analysis of orthologous gene families (OGFs) in the Archaeplastida. a Parsimony-based model of gene family evolution of primary plastid genes based on the reference phylogeny of these plastid genomes (Figs. 1 and 3 and Additional file 8: Figure S23). The 297 OGFs from 3587 cyanobacterial genes were predicted from a database of 329,972 cyanobacterial genes (99 cyanobacteria strains), and are regarded as hypothetical ancestral OGFs of primary plastid genes. The numbers of ancestral OGF homolog groups and genes in glaucophytes (cyan), green lineage (green), and red algae (red) plastid genomes are shown on the right of the taxon name. Each loss (-) and hypothetical ancestral stage of the OGF groups is shown in the tree based on parsimony. Common OGF groups between “ancestral stage of glaucophytes and green lineage” and “red algae” and between “glaucophytes” and “green lineage” are described in each ancestral clade. b Simplified map of gene family loss (-) from plastid genomes and gene transfer (+) to the nuclear genome via endosymbiotic gene transfer (EGT) based on parsimony. PT and Nu indicate plastid- and nuclear-encoded OGFs, respectively. c The total number of gene families that include plastid- and nuclear-encoded OGFs in the three primary plastid groups. Colored numbers indicate nuclear-encoded plastid OGFs, for example, among 127 OGFs, 27 EGTs from glaucophytes, 57 EGTs from Viridiplantae, and four EGTs from red algae (see details in Additional file 1: Table S13)