Table 1.
Enrichment tests of pseudogene and pseudogene parental locus PFAM domains with respect to PFAM domains of functional loci used as queries across the five plant genomes.
| Test | A. thaliana | P. vulgaris | P. trichocarpa | V. vinifera | O. sativa | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PFAM | Family | Odds | PFAM | Family | Odds | PFAM | Family | Odds | PFAM | Family | Odds | PFAM | Family | Odds ratio | |
| Pseudo versus functional | PF007723 | Glycoside hydrolase | 4.01 | PF0076 | RRM1 | 2.72 | PF13676 | TIR | 2.53 | PF00954 | S-locus | 7.34 | PF14288 | FKS1 | 22.48 |
| PF00646 | Fbox | 4.88 | PF14111 | DUF4283 | 10.48 | PF13966 | Zf-RVT | 101.47 | PF01453 | B-lectin | 3.61 | PF02364 | Glucan synthase | 22.48 | |
| PF08387 | FBD | 4.63 | PF08626 | TRAPPC9-Trs120 | 29.22 | PF14111 | DUF4283 | 8.28 | PF00069 | P kinase | 1.4 | PF04983 | Rbp1 | 25.63 | |
| PF07734 | FBA | 5.79 | PF12739 | TRAPP-1 | 29.22 | PF05695 | DUF825 | 48.45 | PF00831 | NB-ARC | 21.45 | PF04998 | AKAP95 | 25.63 | |
| PF08268 | FBA-3 | 5.28 | PF02889 | Sec-63 | 7.5 | PF05695 | DUF825 | 48.45 | PF00831 | NB-ARC | 21.45 | PF04998 | AKAP95 | 25.63 | |
| PF08268 | FBA-3 | 5.28 | PF02889 | Sec63 | 7.5 | PF05970 | PIF1 | 9.03 | PF01582 | TIR | 77.87 | PF13966 | Zf-RVT | 36.14 | |
| PF14392 | Zf-CCHC-4 | 13.21 | PF02892 | zf-BED | 18.95 | PF00560 | LRR-1 | 1.78 | PF05964 | FYRN | 12.4 | PF13456 | RVT-3 | 38.1 | |
| PF14111 | DUF4283 | 16.82 | PF04937 | DUF659 | 18.96 | PF14392 | Zf-CHHC-4 | 5.55 | PF05965 | FYRC | 12.4 | PF00069 | P | Kinase 2.51 | |
| PF13456 | RVT-3 | 8.03 | PF05964 | FYRN | 6.31 | PF13855 | LRR-8 | 1.55 | PF00400 | WD40 | 3.51 | PF00623 | RBp-1 | 20.5 | |
| Parental versus functional | PF07723 | Glycoside hydrolase | 5.49 | PF00931 | NB-ARC | 5.21 | PF00560 | LRR-1 | 2.63 | PF07714 | P-kinase-Tyr | 1.66 | PF13855 | LRR-8 | 3.10 |
| PF00646 | F-box | 7.37 | PF14111 | DUF4283 | 79.49 | PF13855 | LRR-8 | 2.35 | PF00069 | P-kinase | 1.66 | PF08263 | LRRNT-2 | 3.12 | |
| PF08387 | FBD | 6.46 | PF13676 | TIR-2 | 6.51 | PF01535 | PPR | 2.34 | PF08370 | PDR-assoc | 18.96 | PF00069 | P-kinase | 3.11 | |
| PF07734 | FBA | 9.87 | PF08370 | PDR-assoc | 16.62 | PF13041 | PPR-2 | 2.26 | PF00082 | Peptidase-S8 | 7.73 | PF00560 | LRR-1 | 3.08 | |
| PF08268 | FBA-3 | 10.39 | PF14510 | ABC-trans | 15.17 | PF08263 | LRRNT-2 | 2.31 | PF01453 | B-lectin | 5.97 | PF07714 | Pkinase-Tyr | 2.55 | |
| PF12819 | Zf-CCHC-4 | 5.95 | PF13855 | LRR-8 | 2.24 | PF13676 | TIR-2 | 4.22 | PF00005 | ABC-tran | 2.96 | PF12796 | Ank-2 | 3.66 | |
| PF01344 | Kelch-1 | 4.51 | PF01582 | TIR | 10.39 | PF00931 | NB-ARC | 3.10 | PF05922 | Inhibitor-I9 | 7.02 | PF08370 | PDR-Assoc | 18.52 | |
| PF03478 | DUF295 | 10.96 | PF00560 | LRR-1 | 2.17 | PF14432 | DYW | 3.72 | PF00122 | E1-E2-ATPase | 5.62 | PF00005 | ABC-tran | 3.31 | |
Fisher tests: alternative hypotheses for odds ratio>1 and P value<0.05, after Bonferroni correction for multiple testing (enrichment for specific PFAM domain in the pseudogene complement).