Table 1.
GO-term and PFAM enrichment [2-tailed Fisher exact test with FDR-corrected P-values (q) of < 0.05] for genes with dN/dS (ω) > 1, and genes with either microevolutionary frameshifts or nonsynonymous mutations across the 7 sets of serial isolates.
| Category | |||||||
|---|---|---|---|---|---|---|---|
| dN/dS > 1 | GO/PFAM term | Genes ω < 1 | Genes ω > 1 | Fisher P | Q-value | Rel. prop | GO/PFAM description |
| GO: 0003723 | 428 | 25 | 2.26E-04 | 3.04E-02 | 1.95 | RNA binding | |
| GO: 0003735 | 152 | 3 | 7.38E-05 | 1.49E-02 | 5.78 | Structural constituent of ribosome | |
| GO: 0003824 | 1745 | 155 | 8.61E-05 | 1.64E-02 | 1.28 | Catalytic activity | |
| GO: 0005515 | 1100 | 81 | 4.48E-06 | 1.41E-03 | 1.55 | Protein binding | |
| GO: 0005740 | 278 | 11 | 5.08E-05 | 1.06E-02 | 2.88 | Mitochondrial envelope | |
| GO: 0005759 | 160 | 4 | 1.90E-04 | 2.65E-02 | 4.56 | Mitochondrial matrix | |
| GO: 0006412 | 287 | 11 | 2.68E-05 | 6.05E-03 | 2.98 | Translation | |
| GO: 0019693 | 100 | 1 | 3.63E-04 | 4.35E-02 | 11.4 | Ribose phosphate metabolic process | |
| GO:0022626 | 87 | 0 | 1.16E-04 | 1.99E-02 | N/A | Cytosolic ribosome | |
| GO:0022857 | 277 | 13 | 4.08E-04 | 4.70E-02 | 2.43 | Transmembrane transporter activity | |
| GO:0036094 | 724 | 52 | 2.58E-04 | 3.31E-02 | 1.59 | Small molecule binding | |
| GO:0043168 | 689 | 48 | 1.89E-04 | 2.65E-02 | 1.64 | Anion binding | |
| GO:0044281 | 498 | 27 | 1.57E-05 | 3.86E-03 | 2.1 | Small molecule metabolic process | |
| GO:0044391 | 143 | 3 | 2.32E-04 | 3.05E-02 | 5.44 | Ribosomal subunit | |
| GO:0071840 | 1325 | 113 | 2.76E-04 | 3.47E-02 | 1.34 | Cellular component organization or biogenesis | |
| GO:1901362 | 364 | 19 | 1.92E-04 | 2.65E-02 | 2.18 | Organic cyclic compound biosynthetic process | |
| PF00624.20 | 4 | 23 | 6.53E-20 | 7.42E-17 | 0.02 | Flocculin repeat | |
| PF10528.11 | 12 | 10 | 1.87E-05 | 1.07E-02 | 0.13 | GLEYA domain | |
| PF00514.25 | 8 | 8 | 5.72E-05 | 2.17E-02 | 0.11 | Armadillo repeat | |
| Microevolution (Frameshift) | GO/PFAM term | Genes without frameshift | Genes with frameshift | Fisher P | Q-value | Rel. prop | GO/PFAM description |
| GO:0009986 | 30 | 9 | 7.53E-12 | 4.26E-08 | 0.03 | Cell surface | |
| GO:0009987 | 3616 | 17 | 1.20E-05 | 3.38E-02 | 1.7 | Cellular process | |
| PF05001.15 | 0 | 17 | 1.10E-39 | 1.25E-36 | 0 | RNA polymerase Rpb1 C-terminal repeat | |
| PF10528.11 | 13 | 9 | 5.54E-15 | 3.15E-12 | 0.01 | GLEYA domain | |
| PF00399.21 | 24 | 9 | 4.09E-13 | 1.55E-10 | 0.02 | Yeast PIR protein repeat | |
| PF08238.14 | 14 | 6 | 2.64E-09 | 7.49E-07 | 0.02 | Sel1 repeat | |
| PF11765.10 | 6 | 3 | 2.58E-05 | 5.86E-03 | 0.01 | Hyphally regulated cell wall protein N-terminal | |
| PF09770.11 | 0 | 2 | 4.79E-05 | 9.08E-03 | 0 | Topoisomerase II-associated protein PAT1 | |
| Microevolution (nonsynonymous) | GO/PFAM term | Genes without nonsynonymous | Genes with nonsynonymous | Fisher P | Q-value | Rel. prop | GO/PFAM description |
| GO:0009986 | 28 | 11 | 7.88E-10 | 4.45E-06 | 0.06 | Cell surface | |
| PF10528.11 | 12 | 10 | 3.14E-11 | 3.58E-08 | 0.03 | GLEYA domain | |
| PF11765.10 | 4 | 5 | 1.03E-06 | 5.87E-04 | 0.02 | Hyphally regulated cell wall protein N-terminal |
The relative proportion (Rel. prop) was calculated as (number of terms in set 1/number of terms in set 2) × (genes with any terms in set 2/genes with any terms in set 1).