Phylogenomic analyses of archaeal genomes have identified large numbers (1448) of proteins that are distinctive characteristics of either all Archaeaor its various subgroups and whose homologues are not found in other organisms [1]. Six of these proteins are unique to all Archaea whereas 10 others are only missing in N. equitans. A large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobalesand Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens). Based upon the species distributions of these proteins, the evolutionary stages where the genes for these proteins have likely evolved are shown in the right panel. Importantly, 31 of these proteins are uniquely present in virtually all methanogens (including M. kandleri) and 10 additional proteins are only found in different methanogens as well as A. fulgidus. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. These results are at variance with the results of phylogenetic analyses where methanogenic archaea do not form a monophyletic grouping [2;3]. Different proteins that are specific for various subgroups of archaea are listed in the Tables below.

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Table 1: Proteins that are specific for all Archaea

Table 2: Proteins that are specific for Crenarchaeota

Table 3: Proteins that are specific for Euryarchaeota

Table 4: Proteins that are specific for methanogens (Methanoarchaeota)

Table 5: Proteins that are specific to certain subgroups of methanogens

Table 6: Proteins restricted to several archaeal lineages

Table 7. Proteins specific to Sulfolobales

Table 8. Proteins specific to Pyrobaculum and Thermofilum

Table 9.  Proteins specific for particular groups of methanogens

Table 10. Proteins specific for Thermococci

Table 11. Halobacteria-specific proteins that are present in all sequenced genomes.

Table 12. Halobacteria-specific proteins present in three of the four sequenced genomes.

Table 13. Halobacteria-specific proteins present in two of the four sequenced genomes.

Table 14: Proteins specific for Thermoplasmata

Table 15 Archaeal-specific Proteins showing sporadic distribution

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Selected References:

1. Gao B, Gupta RS. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 2007; 8:86.
2. Gribaldo S, Brochier-Armanet C. The origin and evolution of Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci 2006; 361(1470):1007-1022.
3. Bapteste E, Brochier C, Boucher Y. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 2005; 1(5):353-363.

Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (April 2007). http://www.bacterialphylogeny.com/index.html