Table 2. Number of species and genus-specific protein models found after clustering with OrthoMCL and filtering with BLASTn.
| Targets | Module 1 | Module 2 | Module 3 | ||
|---|---|---|---|---|---|
| Non-target genomes | # of protein models | # OrthoMCL clusters | # OrthoMCL unique clusters | # of unique clusters | |
| Phytophthora | |||||
| Species-specific | |||||
| P. ramorum | PINFa, PSOJ, PLAT, PCAP, PCIN, PHIB, PFOL | 52,280b | 1,624 (3.1%) | 37 | |
| P. lateralis | PINF, PSOJ, PRAM, PCAP, PCIN, PHIB, PFOL | 52,280b | 5,578 (10.7%) | 180 | |
| P. kernoviae | PINF, PSOJ, PRAM, PCAP, PCIN | 44,422 | 830 (1.9%) | 55 | |
| Group-specific | |||||
| P. ramorum+P. lateralis | PINF, PSOJ, PCAP, PCIN, PHIB, PFOL | 52,280 | 110 (0.2%) | 9 | |
| Dothideomycetes | |||||
| Species-specific | |||||
| Sphaerulina musiva | STON, SPOP, MPUN, PGAE, MGRAM, MLAR, MGIB, DPIN, DOTS, MDEAR, CLAF, MFIJ | 160,617 | 44,189b | 885 (2.0%) | 131 |
| S. populicola | STON, SMUS, MPUN, PGAE, MGRAM, MLAR, MGIB, DPIN, DOTS, MDEAR, CLAF, MFIJ | 160,617 | 44,189b | 765 (1.7%) | 134 |
| Phaeocryptopus gaeumannii | STON, SMUS, SPOP, MPUN, MGRAM, MLAR, MGIB, DPIN, DOTS, MDEAR, CLAF, MFIJ, CERZ, BAUCO, DIDZE | 193,449 | 51,248b | 3,350 (6.5%) | 1,000 |
| Group-specific | |||||
| S. musiva+S. populicola | STON, MPUN, PGAE, MGRAM, MLAR, MGIB, DPIN, DOTS, MDEAR, CLAF, MFIJ | 160,617 | 44,189 | 392 (0.9%) | 68 |
| S. musiva+S. populicola+ STON1 | STON, MPUN, PGAE, MGRAM, MLAR, MGIB, DPIN, DOTS, MDEAR, CLAF, MFIJ | 160,617 | 44,189 | 345 (0.8%) | 163 |
| Rusts | |||||
| Species-specific | |||||
| Melampsora larici-populina | All Pucciniales genomes in Table S3, but M. larici-populina | 13,355b | 3,550 (26.6%) | 1,519 | |
| M. medusae f. sp. deltoidae | All Pucciniales genomes in Table S3, but M. medusae f. sp. deltoidae | 20,713b | 8,901 (43.9%) | 1,542 | |
| Cronartium ribicola | All Pucciniales genomes in Table S3, but C. ribicola | 9,633b | 2,782 (28.8%) | 1,341 | |
| Genus-specific | |||||
| Melampsora genus | All Pucciniales genomes in Table S3, but Melampsora spp. | 1,870c | 374 (20.0%) | 270 | |
| Cronartium genus | All Pucciniales genomes in Table S3, but Cronartium spp. | 1,027c | 51 (5.0%) | 34 | |
Notes.
Species name abbreviations: PINF, Phytophthora infestans; PSOJ, P. sojae; PCAP, P. capsicii; PCIN, P. cinnamomi var. cinnamomi; PHIB, P. hibernalis; PFOL, P. foliorum; PRAM, P. ramorum; PLAT, P. lateralis; STON, Mycosphaerella sp. STON; SMUS, Sphaerulina musiva; SPOP, S. populicola; PGAE, Phaeocryptopus gaeumannii; MPUN, Ramularia endophylla, MGRAM, Zymoseptoria tritici; MLAR, M. laricina; MGIB, Pseudocercospora pini-densiflorae; DPIN, Dothistroma pini; DOTS, D. septosporum; MDEAR, Lecanostica acicula; CLAF, Cladosporum fulvum; MFIJ, M. fijiensis; CERZ, C. zeae-maydis; BAUCO, Baudoinia compniacensis; DIDZE, Didymella zeae-maydi.
Number of OrthoMCL clusters that include at least one gene from the targeted species.
Number of OrthoMCL clusters that include at least one gene for each species of the genus.