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.
Highlights
Comparative genomics of the bacteria and archea is well developed, has provided many insights, and has promoted the development of numerous analytical tools
Shared Proteins between Dictyostelium and Entamoeba Using the complete predicted protein sets of each organism, we ran reciprocal BLASTP analyses to identify putative orthologs between E. histolytica and D. discodeum, using only proteins that hit a cognate with an e-value of 10À5, and requiring that each protein return its cognate from the other genome as a best hit when used as a query
Using the Homo sapiens, C. elegans, D. melanogaster, Saccharomyces cerevisiae, and Arabidopsis thaliana genomes as the representative model genomes for the other sequenced eukaryotes, we determined that 1,545 of the shared orthologs between D. discoideum and E. histolytica matched orthologs with the other major eukaryotes, with 1,199 genes being universally conserved among all seven representative eukaryotic genomes
Summary
Comparative genomics of the bacteria and archea is well developed, has provided many insights, and has promoted the development of numerous analytical tools. Genomic comparisons from species as divergent as man and the nematode Caenorhabditis elegans have provided important insights into the functional aspects of each genome [1]. Comparing genomes from organisms along a common evolutionary lineage and of varying phylogenetic distances has been informative, and the recent sequencing and comparison of five hemiascomycete yeast genomes best illustrates this. These studies showed how the hemiascomycete lineage was shaped through the forces of massive genome duplication, reductive evolution, and gene dispersion [2]. The comparison of the first two sequenced Drosophila species, D. melanogaster and D. pseudoobscura, has proven so fruitful that 12 additional Drosophila genomes are being sequenced [3]
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