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Table 1 Classification of gene families according to the evolutionary history that explains their origin

From: The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Species Description   Evolutionary events Class
   Clustering DOLLOP CAFE   
    ancestors extant ancestors extant   
F. graminearum Transmembrane transporter X X X X X gain; TP15; enlarged family size; significant expansion C1; C3
  Mannosidase activity X X   X   TP15; enlarged family size C3
  Peptidase activity X   X   X gain; enlarged family size C1
  Transferase activity X   X    gain; enlarged family size C1
  Chitin binding X X   X   TP15; enlarged family size C3
  Lipid metabolism   X X X X gain; TP15 C1; C3
  Methyltransferase activity   X   X X TP15; significant expansion C2
  N-acetyl transferase activity X X   X   TP15; enlarged family size C3
  Oxidoreductase activity X X   X   TP15; enlarged family size C3
  Polyssacharide binding    X   X gain C1
  Chitinase activity    X   X gain C1
  Gluthatione peroxidase    X   X gain C1
  Thioredoxin peroxidase    X   X gain C1
  Astacin activity   X   X   TP15 C3
  G-coupled protein receptor   X   X   TP15 C3
  Tartrate dehydrogenase activity X X   X   TP15; enlarged family size C3
T. reesei Transmembrane transporters    X   X loss C3
  Lipid metabolism    X   X loss C3
  Polyketide biosynthetic pathway    X   X gain  
  Nuclease activity X X   X   gain; enlarged family size  
  Chitin binding    X   X loss C3
  Astacin activity    X   X loss C3
  Fatty-acid synthase activity X X   X   gain; enlarged family size  
  N-acetyl transferase activity    X   X loss C3
  Mannosidase activity    X   X loss C3
  G-coupled protein receptor    X   X loss C3
  Oxidoreductase activity    X   X loss C3
  Tartrate dehydrogenase activity    X   X loss C3
N. crassa Transmembrane transporters    X   X loss C3
  Lipid metabolism    X   X loss C3
  Chitin binding    X   X loss C3
  Astacin activity    X   X loss C3
  N-acetyl transferase activity    X   X loss C3
  Oxidoreductase activity    X   X loss C3
  Mannosidase activity    X   X loss C3
  G-coupled protein receptor    X   X loss C3
  Tartrate dehydrogenase activity    X   X loss C3
M. grisea Mannosidase activity X X   X   TP15; enlarged family size C3
  Peptidase activity X   X   X gain; enlarged family size C1
  G-coupled protein receptor X X X X   TP15; enlarged family size C3
  Chitin binding X X   X   TP15; enlarged family size C3
  Lipid metabolism X X   X   TP15; enlarged family size C3
  Transmembrane transporter   X   X   TP15 C3
  Subtilase activity    X   X gain C1
  Cutinase activity    X   X gain C1
  Polysaccharide binding X   X   X gain; enlarged family size C1
  Chitinase activity X   X   X gain; enlarged family size C1
  Gluthatione peroxidase    X   X gain C1
  Thioredoxin peroxidase    X   X gain C1
  Ribonuclease H   X   X X TP15; significant expansion C2
  RNA-directed DNA polymerase   X   X X TP15; significant expansion C2
  Astacin activity   X   X   TP15 C3
  Polyketide biosynthetic pathway   X X X X gain; TP15; significant expansion C1, C2
A. nidulans Antimicrobial peptide production    X   X gain  
  Transcription factor activity   X   X X gain  
  Light sensing    X   X gain  
  Chitin binding    X   X loss C3
  Astacin activity    X   X loss C3
  Lipid metabolism    X   X loss C3
  Transmembrane transporter    X   X loss C3
  N-acetyl transferase activity    X   X loss C3
  Mannosidase activity    X   X loss C3
  G-coupled protein receptor    X   X loss C3
  Oxidoreductase activity    X   X loss C3
  Tartrate dehydrogenase activity    X   X loss C3
A. oryzae X- Pro dipeptidyl-peptidase activity X   X   X gain; enlarged family size  
  Acid-ammonia ligase activity X   X   X gain; enlarged family size  
  Nuclease activity X X   X   gain; enlarged family size  
  Fatty-acid synthase activity X X   X   gain; enlarged family size  
  Monooxygenase activity    X   X gain  
  Chitin binding    X   X loss C3
  Astacin activity    X   X loss C3
  Lipid metabolism    X   X loss C3
  Transmembrane transporter    X   X loss C3
  Positive regulation of cell growth    X   X loss  
  N-acetyl transferase activity    X   X loss C3
  Mannosidase activity    X   X loss C3
  G-coupled protein receptor    X   X loss C3
  Oxidoreductase activity    X   X loss C3
  Tartrate dehydrogenase activity    X   X loss C3
M.graminicola Transmembrane transporters X X   X X TP15, enlarged family size; significant expansion C3
  Lipid metabolism   X   X   TP15 C3
  Mannosidase activity X X   X   TP15; enlarged family size C3
  Peptidase activity X   X   X gain; enlarged family size C1
  Transferase activity X   X   X gain; enlarged family size C1
  G-coupled protein receptor X X   X   TP15; enlarged family size C3
  Chitin binding X X   X   TP15; enlarged family size C3
  Astacin activity   X X X X gain; TP15 C1; C3
  Proteolytic activity    X   X gain C1
  Phospholipase A2 activity X   X   X gain; enlarged family size C1
  Oxidoreductase activity X X   X   TP15; enlarged family size C3
  N-acetyl transferase activity X X   X   TP15; enlarged family size C3
  Tartrate dehydrogenase activity X X   X   TP15; enlarged family size C3
  Nitrogen catabolism   X   X   loss C4
  Response to nitrogen starvation   X   X   loss C4
  Sensing nitrogen levels   X   X   loss C4
M. fijiensis Transmembrane transporter X X   X   TP15; enlarged family size C3
  Lipid metabolism   X   X   TP15 C3
  Mannosidase activity X X   X   TP15; enlarged family size C3
  Transferase activity X   X   X gain; enlarged family size C1
  G-coupled protein receptor X X   X X TP15; enlarged family size C3
  Metalloexopeptidase activity X   X   X gain; enlarged family size C1
  Proteolytic activity    X   X gain C1
  Astacin activity   X X X X gain; TP15; significant expansion C1; C3
  Glutathione peroxidase    X   X gain C1
  Thioredoxin peroxidase    X   X gain C1
  Chitin binding   X   X X TP15; significant expansion C3
  Nitrogen catabolism   X   X   loss C4
  Sensing nitrogen levels   X   X   loss C4
  Response to nitrogen starvation   X   X   loss C4
  1. Only families for which the evolutionary history was consistently reconstructed by DOLLOP and CAFE are displayed. Description: GO description of the families. Clustering: indicates whether an above the family-average gene copy number was observed in at least one species according to the cluster analysis. Evolutionary events in non-pathogens were not categorized. Family size contractions due to gene loss events that do not imply the entire loss of the gene family were not included in the table but covered in the 'Dating gene duplication and loss events' section. Evolutionary events: 'gains' and 'losses' as inferred by DOLOP and CAFE; 'significant expansion as inferred by CAFE; 'enlarged gene family size' as inferred by clustering i.e. size of the family in the indicated species is larger than the family average. An 'X' indicates whether the event occurred in an ancestral node or in an extant species. Class: Gene families were classified according to the evolutionary event that explains their origin. The four classes (C1-C4) correspond to those shown in Figure 3 and described in the main text.
  2. Remark 1: Non-pathogen-specific gains were never observed.
  3. Remark 2: Although theoretically CAFE should be able to discover significant expansions or contractions of gene families in ancestral species, these were never observed. All cases of significant expansions and contractions were observed in the extant species.
  4. Remark 3: Note that the class distinction was made based on the gene content of the families and not based on their functional annotation. This explains why families belonging to the same GO category can belong to different classes (e.g. some astacin families that were present ancestrally got lost in a non-pathogen-specific way: those belong to C3. Other astacin related families were selectively gained in some pathogens. Those belong to C1.