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Distribution of ORFs among COG categories for complete genomes of Halobacterium sp. and Archaeoglobus fulgidus
Neisseria meningitidis (Neime), Pasteurella multocida (Pasmu), Psudomonas aeruginosa (Pseae), Rickettsia prowazekii (Ricpr), Staphyloccocus aureus (Staau), Streptococcus pyogenes (Strpy), Synechocystis PCC6803 (SynPC), Thermotoga maritima (Thema), Treponema pallidum (Trepa), Ureaplasma urealyticum (Ureur), Vibrio cholerae (Vibch), Xylella fastidiosa (Xylfa), and ten archaea: Aeropyrum pernix (Aerpe), Archaeoglobus fulgidus (Arcfu), Halobacterium sp. (Halsp), Methanobacterium thermoautotrophicum (Metth), Methanococcus jannaschii (Metja), Pyrococcus horikoshii (Pyrho), Pyrococcus abyssi (Pyrab), Sulfolobus solfataricus (Sulso), Thermoplasma acidophilum (Theac), Thermoplasma volcanium (Thevo).
To test for the possibility that long branch attraction [ 48 ] might be the reason for the strong support of Halobacterium sp. grouping with Synechocystis sp., we repeated the analysis replacing the Halobacterium sp. genome with that from Archaeoglobus fulgidus , another archaeon.
These are also the categories in which Halobacterium sp. shows many more OuartOPs in support of topology 3 than A. fulgidus .
Data from the following species were assembled into presumptive orthology groups (hereafter, proteins) and aligned [ 36 ] : Aquifex aeolicus , Bacillus subtilis , Borrelia burgdorferi , Chlamydia trachomatis , Escherichia coli , Haemophilus influenzae , Helicobacter pylori, Mycobacterium tuberculosis, Mycoplasma genitalium, Mycoplasma pneumoniae , Rickettsia prowazekii, Synechocystis sp., and Treponema pallidum (Eubacteria), Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Pyrococcus abyssi , and P. horikoshii (Archaebacteria: Euryarchaeota), and Arabidopsis thaliana, Caenorhabditis elegans, Dictyostelium discoideum, Drosophila melanogaster, Gallus gallus, Homo sapiens, Mus musculus, Oryza saticva, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma sp. , and Xenopus laevis (Eukaryota).
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