The group includes eukaryotic cells that, for the most part, have a single emergent flagellum, or are amoebae with no flagella. The unikonts include opisthokonts (animals, fungi, and related forms) and Amoebozoa. By contrast other well-known eukaryotic groups, which more often have two emergent flagella (although there are many exceptions) are often referred to as bikonts. Bikonts include Archaeplastida (plants and relatives), Excavata, Rhizaria, and Chromalveolata.
The unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts, but not bacteria or bikonts, encode enzymes for synthesis of the pyrimidine nucleotides: carbamoyl phosphate synthase, dihydroorotase, aspartate carbamoyltransferase. This must have involved a double fusion, a rare pair of events, supporting the shared ancestry of Opisthokonta and Amoebozoa.
Cavalier-Smith  originally proposed that unikonts ancestrally had a single flagellum and single basal body. This is unlikely, however, as flagellated opisthokonts, as well as some flagellated Amoebozoa, including Breviata, actually have two basal bodies, as in typical 'bikonts' (even though only one is flagellated in most unikonts). This paired arrangement can also be seen in the organization of centrioles in typical animal cells. In spite of the name of the group, the common ancestor of all 'unikonts' was probably a cell with two basal bodies.
- Cavalier-Smith T (March 2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". Int. J. Syst. Evol. Microbiol. 52 (Pt 2): 297–354. PMID 11931142.
- Cavalier-Smith, Thomas (2003). "Protist phylogeny and the high-level classification of Protozoa". European Journal of Protistology 39 (4): 338–348. doi:10.1078/0932-4739-00002.
- A Minge M, Silberman JD, Orr RJ et al. (November 2008). "Evolutionary position of breviate amoebae and the primary eukaryote divergence". Proc. Biol. Sci. 276 (1657): 597–604. PMC 2660946. PMID 19004754. doi:10.1098/rspb.2008.1358.
- Burki F, Pawlowski J (October 2006). "Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts". Mol. Biol. Evol. 23 (10): 1922–30. PMID 16829542. doi:10.1093/molbev/msl055.
- Glücksman E, Snell EA, Berney C, Chao EE, Bass D, Cavalier-Smith T (September 2010). "The Novel Marine Gliding Zooflagellate Genus Mantamonas (Mantamonadida ord. n.: Apusozoa)". Protist 162 (2): 207–221. PMID 20884290. doi:10.1016/j.protis.2010.06.004.
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