Table 3.
The pan-genomes of Corallococcus, Group A Corallococci, Group B Corallococci, and Myxococcus.
| Corallococcus spp. | Group A Corallococci | Group B Corallococci | Myxococcus spp. | |
|---|---|---|---|---|
| Genomes (n) | 24 | 17 | 7 | 6 |
| # discrete species | 9–11 | 5–6 | 4–5 | 6 |
| Mean genes per genome | 8,161 | 8,162 | 8,157 | 7,286 |
| Pan-genome size (genes) | 43,561 | 26,491 | 21,292 | 23,833 |
| Average % of genes in the core | 30.5% | 51.4% | 40.2% | 8.4% |
| Core genes (total) (%) | 2,486 (5.7%) | 4,195 (15.8%) | 3,282 (15.4%) | 609 (2.6%) |
| -Core genes (hard) (%) | -2,315 (5.3%) | -4,195 (15.8%) | -3,282 (15.4%) | -609 (2.6%) |
| -Core genes (soft) (%) | -171 (0.4%) | -0 (0%) | -0 (0%) | -0 (0%) |
| Accessory genes (total) (%) | 41,075 (94.3%) | 22,296 (84.2%) | 18,010 (84.6%) | 23,224 (97.4%) |
| -Accessory genes (shell) (%) | -9,846 (22.6.0%) | -7,471 (28.2%) | -8,009 (37.6%) | -23,224 (97.4%) |
| -Accessory genes (cloud) (%) | -31,229 (71.7%) | -14,825 (56.0%) | -10,001 (47.0%) | -0 (0%) |
| Extrapolated pan-genome (new genes) when n = 101 | 101,987 (555) | 55,378 (228) | 77,244 (372) | 121,349 (747) |
| Extrapolated pan-genome (new genes) when n = 501 | 245,333 (269) | 107,520 (89) | 167,900 (163) | 327,798 (406) |
| Extrapolated pan-genome (new genes) when n = 1001 | 358,522 (196) | 143,228 (59) | 234,844 (114) | 503,647 (312) |
| Extrapolated core genes at n = ∞ | 988 (39.7%) | 4,058 (96.7%) | 3,105 (94.6%) | 405 (66.5%) |
| COGs enriched in core genome | E F H J | E F I | F J | E F J |
| COGs enriched in accessory genome | Q V | L Q V | Q | P Q |
| BGCs for named metabolites – core | 5 (10.0%) | 5 (15.6%) | 6 (18.2%) | 7 (26.9%) |
| BGCs for named metabolites – accessory | 45 (90.0%) | 27 (84.4%) | 27 (81.8%) | 19 (73.1%) |
For each pan-genome, the composition is presented, together with extrapolations to larger numbers of included genomes, and the number of biosynthetic gene clusters (BGCs) with similarity to those producing named compounds. COG categories enriched in particular sub-pan-genomes are: E, amino acid transport and metabolism; F, nucleotide transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; L, replication, recombination and repair; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; and V, defense mechanisms.