TABLE 2.
Top-ranked genes with the largest evolved increases in gene expression and their knockout phenotypes
| Gene IDa | FCD (stages)b | Putative function (gene product) | Knockout phenotype | Rank | Source or reference |
|---|---|---|---|---|---|
| FGRRES_17170 | 80.3 (S0−S1) | Oxidoreductase (PGLX) | Perithecia pigment | 1 | Frandsen et al. (51) |
| FGRRES_02305 | 42.2 (S0−S1) | Aminohydrolase | Wild type | 3 | This study |
| FGRRES_00262 | 13.4 (S0−S1) | Hypothetical protein | Wild type | 14 | This study |
| FGRRES_08061 | 10.2 (S0−S1) | Phosphoenolpyruvate carboxykinase | Wild type | 18 | This study |
| FGRRES_00348 | 9.5 (S0−S1) | Argonaute 2 (AGO2) | Fewer asci/ascospore | 22 | Kim et al. (24) |
| FGRRES_08576 | 9.5 (S0−S1) | Meiotic cohesin (yeast rec8) | Aborted and less ascospores | 23 | This study |
| FGRRES_00503 | 18.7 (S1−S2) | O-Succinylhomoserine lyase | Wild type | 11 | This study |
| FGRRES_03365 | 13.9 (S1−S2) | Nuclease/phosphatase family | Wild type | 13 | This study |
| FGRRES_10126 | 11.5 (S1−S2) | Propionyl-CoA synthetase | Wild type | 16 | This study |
| FGRRES_05439 | 10.1 (S1−S2) | Hypothetical protein | Wild type | 19 | This study |
| FGRRES_06533 | 9.6 (S1−S2) | Hypothetical protein | No perithecia | 20 | This study |
| FGRRES_06797 | 9.6 (S1−S2) | Hypothetical protein | No paraphyses and asci | 21 | This study |
| FGRRES_03356 | 9.5 (S1−S2) | Hypothetical protein | Wild type | 24 | This study |
| FGRRES_06285 | 7.5 (S1−S2) | α/β-Hydrolase superfamily | No paraphyses and asci | 36 | This study |
| FGRRES_16442 | 41.4 (S2−S3) | Oxidoreductase | Wild type | 4 | This study |
| FGRRES_09307 | 31.1 (S2−S3) | Hypothetical protein | Aborted and less ascospores | 7 | This study |
| FGRRES_07376 | 22.0 (S2−S3) | Copper homeostasis protein | Wild type | 9 | Trail et al. (10) |
| FGRRES_09973 | 20.6 (S2−S3) | Tyrosine phosphatase | Wild type | 10 | This study |
| FGRRES_00526 | 11.1 (S2−S3) | Dihydroneopterin aldolase | Wild type | 17 | This study |
| FGRRES_01058 | 56.4 (S3−S4) | Serine threonine kinase (PUK1) | Abnormal ascospores | 2 | Wang et al. (21) |
| FGRRES_17271 | 35.8 (S3−S4) | RNA-binding protein (yeast spo5) | No ascospore | 6 | This study |
| FGRRES_04345 | 29.5 (S3−S4) | Aspartic protease | Wild type | 8 | This study |
| FGRRES_05400 | 18.4 (S3−S4) | Glycoside hydrolase family 16 | Defects in ascospore release | 12 | This study |
| FGRRES_10224 | 13.2 (S3−S4) | Hypothetical protein | Wild type | 15 | This study |
| FGRRES_17505 | 9.1 (S3−S4) | Asparaginase family protein | Defects in ascospore release | 25 | This study |
| FGRRES_17508 | 7.7 (S3−S4) | Hypothetical protein | No ascospore | 35 | This study |
| FGRRES_17498 | 39.9 (S4−S5) | sugar transporter | Wild type | 5 | This study |
a
Gene ID based on the Ensembl annotation version 32 of Fusarium graminearum wild-type strain PH-1.
b
Fold change differentials (FCD) were calculated as max [(Xt+1 – Xt) − (Yt+1 – Yt)], where t represents the developmental stages (0 to 4), X is the LOX-transformed expression level of an extant species (e.g., F. graminearum), and Y is the inferred expression level of the most recent common ancestor (MRCA) of the five species: C. globosum, F. graminearum, F. neocosmosporiellum, M. oryzae, and N. crassa.