Table 6.
Distribution of all switchgrass genes and genes with copy number and presence/absence variation in switchgrass-specific genes and core ortholome in grass species
| Genotype | Total up-CNVs | Total down-CNVs | Total PAVs | Switchgrass-specific genes |
Core ortholome in grass species |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Total number of switchgrass-specific genes (%) | Up-CNVs in switchgrass-specific gene family (%) | Down-CNVs in switchgrass-specific gene family (%) | PAVs in switchgrass-specific gene family (%) | Total number of switchgrass genes conserved among grass species (%) | Up-CNVs in conserved genes (%) | Down-CNVs in conserved genes (%) | PAVs in conserved genes (%) | ||||
| A5 | 109 | 2432 | 914 | 69 (63.3) | 1113 (45.8) | 463 (50.7) | 12 (11.0) | 427 (17.6) | 85 (9.3) | ||
| SG5 | 101 | 2236 | 1047 | 60 (59.4) | 1007 (45.0) | 522 (49.9) | 10 (9.9) | 408 (18.2) | 99 (9.5) | ||
| W4 | 342 | 1806 | 1113 | 178 (52.0) | 966 (53.5) | 558 (50.1) | 37 (10.8) | 358 (19.8) | 121 (10.9) | ||
| Car1 | 186 | 2501 | 1152 | 23 811 (36.1) | 113 (60.8) | 1132 (45.3) | 559 (48.5) | 29 759 (45.2) | 27 (14.5) | 392 (15.7) | 87 (7.6) |
| P2 | 325 | 1179 | 827 | 160 (49.2) | 644 (54.6) | 430 (52.0) | 31 (9.5) | 211 (17.9) | 57 (6.9) | ||
| She2 | 116 | 2398 | 1249 | 70 (60.3) | 1068 (44.5) | 610 (48.8) | 15 (12.9) | 407 (17.0) | 102 (8.2) | ||
| Tr5 | 346 | 1307 | 961 | 187 (54.0) | 685 (52.4) | 510 (53.1) | 36 (10.4) | 248 (19.0) | 79 (8.2) | ||
In total, 65 878 switchgrass genes were used in these analyses. To determine switchgrass-specific genes and core ortholome among grass species, predicted switchgrass proteins were used along with the predicted proteomes of rice, maize, sorghum, Setaria, and Brachypodium in OrthoMCL analyses as described in the Experimental Procedures. When genes are conserved in the all six Poaceae species, they are defined as core ortholome.