Table 1.
Number of genes strictly shared (as determined by reciprocal best match) within major taxa of prokaryotesa
|
Prokaryotes: 14.82 (sd = 2.55), range 10-23, n = 147 |
| Archaea: 144.53 (sd = 8.00), range 128-156, n = 17 |
| Crenarchaeota: 587.75 (sd = 5.91), range 582-596, n = 4 |
| Euryarchaeotab: 174.00 (sd = 5.95), range 165-182, n = 12 |
| Bacteria: 61.53 (sd = 2.71), range 56-70, n = 130 |
| Bacteroidetes: 1219.00 (sd = 4.24), range 1216-1222, n = 2 |
| Chlamydia: 780.57 (sd = 1.81), range 778-784, n = 7 |
| Cyanobacteria: 820.50 (sd = 23.53), range 776-844, n =8 |
| High-G + C Firmicutes: 349.25 (sd = 11.99), range 327-363, n = 12 |
| Low-G + C Firmicutesc: 118.74 (sd = 3.56), range 109-125, n = 35 |
| Bacillus/Streptococcus group: 478.48 (sd = 11.86), range 446-491, n = 23 |
| Clostridium/Fusobacterium group: 466.20 (sd = 16.02), range 444-485, n = 5 |
| Mollicutesd: 236.83 (sd = 8.98), range 220-245, n = 6 |
| Proteobacteria: 131.47 (sd = 4.66), range 124-141, n = 58 |
| α: 456.54 (sd = 12.89), range 434-472, n = 11 |
| β + γ: 195.58 (sd = 7.41), range 185-213, n = 41 |
| ϵ: 787.40 (sd = 5.32), range 780-793, n = 5 |
| Spirochaetes: 321.00 (sd = 8.00), range 313-329, n = 3
|
| Clades were defined from a genomic phylogeny based on the mean normalized BLASTP similarity between pairs of genomes (Clarke et al. 2002; Charlebois et al. 2004), but with preferential weighting in favor of phylogenetically concordant sequences (Gophna et al. 2004). Reported are means: from the perspective of each genome in a clade, the size and composition of the shared set of genes is somewhat variable, owing to match threshold effects. For instance, the union of the set of genes shared by all 147 prokaryotic genomes (at the time of this analysis) has 30 members (see Table 3), despite the mean number of genes shared by all represented prokaryotes being only 14.8. |
-
↵a Using the “Find ubiquitous genes” query within NGIBWS (Charlebois et al. 2003), and a BLASTP cutoff threshold value of 1.0e-5
-
↵b Including Nanoarchaeum equitans, but excluding Halobacterium salinarum NRC-1 which branches basally to other Archaea in our phylogenies
-
↵c Including Fusobacterium nucleatum
-
↵d Excluding Phytoplasma asteris, which branches basally to the Bacillus/Streptococcus group in our phylogenies
