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

Sánchez-Rodríguez, Aminael; Martens, Cindy; Engelen, Kristof; Van de Peer, Yves; Marchal, Kathleen

doi:10.1186/1471-2148-10-318

BMC Ecology and Evolution

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

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.
Remark 1: Non-pathogen-specific gains were never observed.
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.
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.

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