title: Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage.
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.
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Song
authors.forename: Qikai
authors.initials: Q
authors.lastname: Xu
authors.forename: Rolf
authors.initials: R
authors.lastname: Olsen
authors.forename: William F
authors.initials: WF
authors.lastname: Loomis
authors.forename: Gad
authors.initials: G
authors.lastname: Shaulsky
authors.forename: Adam
authors.initials: A
authors.lastname: Kuspa
authors.forename: Richard
authors.initials: R
authors.lastname: Sucgang
mesh_terms: D000818:Animals; D004023:Dictyostelium / Q000145:classification* / Q000235:genetics*; D004747:Entamoeba / Q000145:classification* / Q000235:genetics*; D017125:Genes, Protozoan / Q000235:genetics*; D018503:Genome, Protozoan / Q000235:genetics*; D006801:Humans; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D020543:Proteome / Q000235:genetics; D015800:Protozoan Proteins / Q000145:classification / Q000235:genetics; D013997:Time Factors
chemical_list: D020543:Proteome; D015800:Protozoan Proteins