Table 3.
Results of mapping CEGs against the genomes of various eukaryotes
| Species | Genome size (Gb) | Coverage | Full-length mapped CEGs (%) | CEGs in annotations (%) | Full-length + partially mapped CEGs (%) | Paralogy index (%) | G1 Map (%) | G4 Map (%) | G1 Identity (%) | G4 Identity (%) |
|---|---|---|---|---|---|---|---|---|---|---|
| Mammals (placental) | ||||||||||
| Canis familiaris | 2.532 | 7.5× | 243 (98.0) | 241 (97.2) | 247 (99.6) | 37.4 | 100 | 96.9 | 38.2 | 65.5 |
| Bos taurus | 3.247 | 7.1× | 244 (98.4) | 243 (98.0) | 246 (99.2) | 33.3 | 98.5 | 95.4 | 37.8 | 65.1 |
| Pan troglodytes | 3.350 | 6.6× | 240 (96.8) | 241 (97.2) | 247 (99.6) | 39.6 | 100 | 96.9 | 38.1 | 65.1 |
| Macaca mulatta | 3.097 | 5.3× | 238 (96.0) | 237 (95.5) | 248 (100) | 36.6 | 100 | 100 | 38.0 | 65.1 |
| Felis catus | 3.000 | 2× | 144 (58.1) | – | 188 (75.8) | 17.4 | 69.7 | 75.4 | 36.3 | 61.1 |
| Loxodonta africana | 3.718 | 2× | 114 (46.0) | – | 170 (68.5) | 15.8 | 65.2 | 64.6 | 34.3 | 59.0 |
| Cavia Porcellus | 3.414 | 1.9× | 114 (46.0) | – | 169 (68.1) | 17.5 | 65.2 | 67.7 | 33.7 | 58.7 |
| Vertebrates | ||||||||||
| Ornithorynchus anatinus | 2.073 | 6× | 185 (74.6) | 175 (70.6) | 210 (84.7) | 27.1 | 75.7 | 86.1 | 35.7 | 63.9 |
| Gallus gallus | 1.100 | 6.6× | 208 (83.9) | 204 (82.3) | 212 (85.4) | 13.0 | 83.1 | 87.7 | 38.0 | 64.6 |
| Xenopus tropicalis | 1.511 | 7.7× | 237 (95.6) | 217 (87.5) | 243 (98.0) | 24.6 | 98.5 | 96.9 | 38.7 | 65.0 |
| Takifugu rubripes | 0.393 | 8.7× | 243 (98.0) | 235 (94.7) | 248 (100) | 20.6 | 98.5 | 100 | 38.4 | 65.4 |
| Insects | ||||||||||
| Anopheles gambiae | 0.278 | 10.2× | 245 (98.8) | 243 (98.0) | 247 (99.6) | 9.4 | 100 | 98.4 | 37.6 | 66.1 |
| Apis mellifera | 0.231 | 7.5× | 228 (91.9) | 173 (69.7) | 243 (98.0) | 6.1 | 98.5 | 98.4 | 38.7 | 65.9 |
| Nematodes | ||||||||||
| Caenorhabditisbriggsae | 0.108 | 12× | 246 (99.2) | 242 (97.6) | 247 (99.6) | 8.1 | 100 | 98.4 | 35.0 | 62.9 |
| Caenorhabditis brenneri | 0.150 | 9.5× | 245 (98.8) | – | 248 (100) | 53.5 | 98.5 | 98.4 | 34.6 | 62.1 |
| Caenorhabditis remanei | 0.152 | 9× | 238 (96.0) | – | 245 (98.8) | 15.5 | 98.5 | 100 | 34.9 | 62.9 |
| Trichinella spiralis | 0.065 | >30× | 233 (94.0) | – | 238 (96.0) | 7.7 | 97.0 | 98.4 | 34.8 | 61.5 |
| Chordates | ||||||||||
| Ciona intestinalis | 0.173 | 11× | 239 (96.4) | 203 (81.8) | 243 (98.0) | 6.3 | 95.5 | 100 | 37.5 | 64.8 |
| Plants | ||||||||||
| Populus trichocarpa | 0.480 | 7.5× | 244 (98.4) | 246 (99.2) | 248 (99.6) | 71.3 | 100 | 100 | 35.0 | 62.1 |
| Oryza sativa | 0.430 | – | 244 (98.4) | 185 (74.6) | 246 (99.2) | 51.6 | 98.5 | 98.4 | 34.2 | 61.4 |
| Chlamydomonas reinhardtii | 0.120 | 12.8× | 231 (93.1) | 221 (89.1) | 233 (94.0) | 6.9 | 87.9 | 98.4 | 31.7 | 59.7 |
| Fungi | ||||||||||
| Neurospora crassa | 0.039 | >10× | 245 (98.8) | 236 (95.1) | 245 (98.8) | 3.7 | 97.0 | 100 | 33.3 | 58.8 |
| Magnoporthe grisea | 0.040 | 7× | 243 (97.9) | 237 (95.5) | 246 (99.6) | 4.1 | 98.5 | 98.4 | 33.0 | 59.3 |
| Protozoan | ||||||||||
| Plasmodium falciparum | 0.023 | – | 186 (75.0) | 204 (82.2) | 187 (75.4) | 4.3 | 56.1 | 96.9 | 25.6 | 52.4 |
| Giardia lamblia | 0.011 | 11× | 115 (46.4) | 135 (54.4) | 115 (46.4) | 3.4 | 18.2 | 67.7 | 26.7 | 44.7 |
Genome sizes are estimates from experimental data. Coverage refers to approximate values of sequence coverage for WGS genomes only. The ‘Full-length mapped CEGs’ column lists numbers and percentages (in parentheses) of the 248 CEGs that were mapped in the genome of each species. ‘CEGs in annotations’ refers to the number of CEGs found in the current set of gene annotations (when available) for each genome. The ‘Full-length + partially mapped CEGs’ column corresponds to the number of full-length CEGs that were mapped (column 4) plus the numbers of CEG fragments that were mapped. The ‘Paralogy index’ indicates the fraction of mapped CEGs for which we detected at least one potential paralog. G1 and G4 mapped percentage corresponds to the number of CEGs from the conservation groups (in Table 3) that have been partially mapped. G1 and G4 identity percent corresponds to the average percentage identity of the global pairwise alignment of the predicted CEGs against the CEGs of the six original species. The latest available versions of genomes were used for this analysis (see Supplementary Table S6 for more details) apart from C. intestinalis for which the v1.95 assembly was used. Genome sizes are estimates. Coverage refers to approximate values of sequence coverage for WGS genomes only.