Table 1.
Lineage-Specific Genes in Amoebas versus Yeasts
Figure 1.
Shared Gene Archetypes between Amoeba and Other Eukaryotes
The combined RBH and TribeMCL clustering identified 1,510 gene archetypes between E. histolytica and D. discoideum, with all but 63 shared with five other model eukaryotes. This Venn diagram illustrates how the shared archetypes are distributed with other eukaryotic genomes; the amoeba-specific genes are not displayed here. Animals are represented by H. sapiens, C. elegans, and D. melanogaster. Plant is represented by A. thaliana, and yeast by S. cerevisiae.
Figure 2.
Proteome-Based Phylogeny of Eukaryotes
Abbreviations for organisms are as follows: Ag, A. gambiae; At, A. thaliana; Ce, C. elegans; Cr, C. rheinhardtii; Ci, C. intestinales; Cp, C. parvum; Cm, C. morolae; Dd, D. discoideum; Dm, D. melanogaster; Eg, E. gracilis; Eh, E. histolytica; Fr, F. rubripes; Gl, G. lamblia; Hs, H. sapiens; Lm, L. major; Nc, N. crassa; Os, O. sativa; Pf, P. falciparum; Sc, S. cerevisiae; Sp, S. pombe; Tt, T. thermophila; Tc, T. cruzi; and Zm, Z. mays. 1 Darwin = 1/2000 of the divergence between S. cerevisiae and H. sapiens. Branch thickness is proportional to the size of each clade. The tree was constructed by full maximum likelihood with clusters of orthologs generated from whole proteomes from each of the organisms. A phylogeny program used for constructing a new amino acid replacement model (23) determined the individual nodes and branch lengths.