Table 2.
Count of variable genes belonging to predicted functional categories across lupin-infecting isolates. Genes unique to lupin-infecting isolates were grouped into functional categories predicted by SignalP, EffectorP or Pfam (Additional file 2). Isolate-specificity was determined within sequences with predicted presence-absence variation (PAV) relative to their respective reference isolate, or by non-orthology (N-O) between the gene sets of isolates of the same species (Additional file 4)
| Species | Botrytis cinerea | Sclerotinia sclerotiorium | ||||
|---|---|---|---|---|---|---|
| Isolate abbreviation | Bcin-Lang | Sscl-Lang | Sscl-Lmut | |||
| Method | PAV | N-O | PAV | N-O | PAV | N-O |
| Count of Signal P (secreted) | 17 | 98 | 0 | 10 | 0 | 18 |
| Count of signal p with Effector P (score > 0.8) | 2 | 22 | 0 | 5 | 0 | 3 |
| Protein repeat motifs (PF00023, PF13606, PF12796, PF00132, PF13374, PF13424, PF00400, PF07676, PF13637) | 1 | 18 | 0 | 9 | 0 | 11 |
| Membrane transport (PF00664, PF00005, PF13520, PF01544, PF07690, PF01566, PF00083, PF05653, PF01061, PF01554, PF13246) | 3 | 16 | 0 | 2 | 0 | 2 |
| Domains of unknown function (PF11807, PF11905, PF05670, PF10067, PF07350, PF11913, PF12013, PF01424, PF02656, PF11917, PF12520, PF16297, PF17107, PF06726, PF14087, PF13054, PF04577, PF11327, PF12051, PF12311) | 4 | 9 | 0 | 5 | 0 | 6 |
| Transposon-related (PF00075, PF03732, PF07727, PF05699, PF00078, PF03221, PF03184, PF13358) | 0 | 6 | 1 | 7 | 1 | 0 |
| Bacteriophage-related (PF05840, PF02925, PF02305, PF02306, PF04687, PF04726) | 6 | 6 | 5 | 0 | 5 | 0 |
| Transcription factors (PF00172, PF04082, PF11951, PF00319, PF00170) | 4 | 12 | 0 | 0 | 0 | 1 |
| Cytochrome P450 (PF00067) | 3 | 14 | 0 | 1 | 0 | 2 |
| Methyltransferase (PF01035, PF13489, PF13649, PF00891, PF12847, PF08242, PF08241) | 0 | 9 | 0 | 0 | 0 | 3 |
| Heterokaryon incompatibility (HET) (PF06985, PF14479) | 0 | 10 | 0 | 4 | 0 | 1 |
| Secondary metabolite synthesis (PF00550, PF03936, PF11991, PF04820, PF08659, PF14765) | 0 | 7 | 0 | 0 | 0 | 3 |
| Transcriptional regulation (PF14420, PF05712, PF05368, PF03226) | 4 | 7 | 0 | 0 | 0 | 1 |
| Ubiquitinilation (PF12861, PF14570, PF13639, PF00240, PF00179, PF01485, PF01088, PF09792) | 1 | 7 | 0 | 0 | 0 | 1 |
| Zinc-binding dehydrogenase (PF00107, PF13602) | 1 | 5 | 0 | 0 | 0 | 4 |
| Protein kinase domain (PF00069) | 0 | 1 | 0 | 1 | 0 | 2 |
| NB-ARC domain (PF00931) | 0 | 1 | 0 | 9 | 0 | 0 |
| AAA family (PF13086, PF13087, PF00004, PF13191) | 1 | 7 | 0 | 1 | 0 | 1 |
| Glycosyl hydrolase (PF16499, PF00933, PF03659, PF04616, PF01532, PF00295, PF00840, PF00150, PF00332) | 2 | 4 | 0 | 0 | 0 | 2 |
| FAD binding/metabolism (PF01494, PF01266, PF08022, PF01565, PF00970) | 1 | 5 | 0 | 0 | 0 | 1 |
| Acetyltransferase (PF00698, PF07247, PF00583, PF13508) | 1 | 4 | 0 | 1 | 0 | 2 |
| Alpha/beta hydrolase (PF12697, PF07859, PF00561) | 2 | 4 | 0 | 0 | 0 | 0 |
| Intronic endonuclease (PF13391, PF07453, PF07460, PF14529) | 1 | 2 | 0 | 3 | 0 | 0 |
| NAD binding/metabolism (PF13450, PF13460, PF00146, PF01370, PF00724) | 3 | 3 | 0 | 0 | 0 | 0 |
| Beta-ketoacyl synthase (PF00109,PF02801) | 0 | 2 | 0 | 0 | 0 | 1 |
| Alcohol dehydrogenase GroES-like domain (PF08240) | 0 | 4 | 0 | 0 | 0 | 2 |
| Dynamin family (PF00350) | 1 | 5 | 0 | 0 | 0 | 0 |
| NACHT domain (PF05729) | 0 | 0 | 0 | 4 | 0 | 2 |
| GMC oxidoreductase (PF00732, PF05199) | 0 | 4 | 0 | 1 | 0 | 0 |
| Carboxyleterase (PF00135) | 1 | 4 | 0 | 0 | 0 | 0 |
| Coenzyme A metabolism (PF00441, PF07993, PF02771, PF02515) | 0 | 4 | 0 | 0 | 0 | 0 |
| Enoyl-(Acyl carrier protein) reductase (PF13561) | 1 | 3 | 0 | 0 | 0 | 0 |
| Tannase and feruloyl esterase (PF07519) | 0 | 4 | 0 | 0 | 0 | 0 |
| AMP-binding enzyme (PF00501) | 0 | 3 | 0 | 0 | 0 | 0 |
| DnaJ domain (PF00226) | 1 | 2 | 0 | 0 | 0 | 0 |