General concepts in the evolution of the eukaryotes

The two alternative scenarios of eukaryogenesis. (a) The archaezoan scenario; (b) the symbiogenesis scenario. The putative archaeal or archaezoan hosts of the α-proteobacterial endosymbiont are shown with elements of their cytoskeleton and cell division apparatus colored as in Figure 4.

Possible archaeal origins of eukaryotic genes. The archaeal tree is shown as a bifurcation of Euryarchaeota and the putative second major branch combining Crenarchaeota, Thaumarchaeota, and Korarchaeota [127]; deep, possibly extinct lineages are shown as a single stem.

Evolution of the eukaryotes. The relationship between the five eukaryotic supergroups - Excavates, Rhizaria, Unikonts, Chromalveolates and Plantae - are shown as a star phylogeny with LECA placed in the center. The 4,134 genes assigned to LECA are those shared by the free-living excavate amoeboflagellate Naegleria gruberi with representatives of at least one other supergroup [67]. The numbers of these putative ancestral genes retained in selected lineages from different supergroups are also indicated. Branch lengths are arbitrary. Two putative root positions are shown: I, the Unikont-Bikont rooting [56,57]; II, rooting at the base of Plantae [60].

Apparent complex origins of some key functional systems of eukaryotes. The likely origins of proteins and domains are shown by color code for three key functional systems of the eukaryotic cell: (a) B-family DNA polymerases comprising the core of the replication apparatus (triangles show Zn-finger modules; crosses indicate inactivated enzymatic domains; pol, polymerase; exo, exonuclease) [100]; (b) RNA interference (RNAi) machinery (RdRp, RNA-dependent RNA polymerase) [70]; and (c) cell division apparatus (the Vps4 ATPase and Snf7-like proteins comprise the ESCRT-III machinery) and cytoskeleton [97,98,105,113]. The domains are not drawn to scale. The light blue color of the three amino-terminal domains of Polε indicates the substantial sequence divergence from the homologous domains of other eukaryotic polymerases.

Breakdown of the genes from two eukaryotes by the putative evolutionary affinities. (a) Yeast and (b) red algae. The putative origin of genes was tentatively inferred from the best hits obtained by searching the NCBI non-redundant protein sequence database using the BLASTP program [125], with all protein sequences from the respective organisms used as queries. Although sequence similarity searches are often regarded as a very rough approximation of the phylogenetic position [126], the previous analysis of the yeast genome showed a high level of congruence between the best hits and phylogenomic results [78]. Major archaeal and bacterial groups are color-coded and denoted 1 to 18; the number of proteins with the best hit to the given groups is indicated. The groups are: 1, Euryarchaeota; 2, Crenarchaeota-Thaumarchaeota-Nanoarchaeota; 3, Firmicutes; 4, γ-Proteobacteria; 5, α-Proteobacteria; 6, δ- and ε-Proteobacteria; 7, β-Proteobacteria; 8, unclassified Proteobacteria; 9, Cyanobacteria; 10, Actinobacteria; 11, Bacteroides-Chlorobi group; 12, Chloroflexi; 13, Planctomycetes; 14, Verrucomicrobia-Chlamydiae-Spirochetes; 15, Deinococcus-Thermus group; 16, Aquificacae and Thermotogae; 17, other bacteria; 18, no archaeal or bacterial homologs.