Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

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Abstract
The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies. Most single-celled eukaryotes were lumped together in a single catchall classification until molecular sequencing revealed that they are a very diverse group that illustrates the different paths eukaryotic evolution has taken. Comparing a representative subset of genes indicates that one group in particular, the Amoebozoa, are a sister group to the animals and fungi, even more closely related than the plants. Despite their diversity, few simple eukaryotes have been the subject of complete genome sequencing. The genomes of two amoebozoa, Dictyostelium discoideum (a free-living social amoeba) and Entamoeba histolytica (a pathogenic amoeba), were recently completed. The authors compared the predicted proteins encoded by each organism to each other, and to other representative eukaryotes, and built a phylogenetic tree using not just a few representative genes, but the entire genomes of 23 organisms. The resulting tree closely re-created the relationships predicted from the sampled genes, including reinforcing the close relationship between the amoebozoa and the animals and fungi. The authors also found very few genes that are exclusively inherited by amoebozoa. Since some amoebozoa are important clinical pathogens, these genes are likely good targets for therapeutic agents that will not affect the animal host.