Table 1.

Dataset used for the analysis of resistance durability and diversity and evolutionary constraints of avirulence factors.

Plant		Virus					Resistance durability				Avirulence factor variables			Selected references**
Crop	Resistance gene*	Species	Genus	Avirulence factor†	Number of sequence	EP‡	Timescale of protection efficiency	Status of the resistance	Virulent isolates	Resistance durability class	Nucleotide diversity§	Amino acid diversity§	ω ratio¶
Pepper	Tsw	TSWV	Tospovirus	NSs	28	7	1 year	Broken down	Common	1	0.034	0.036	0.291	Margaria et al. (2007)
Tomato	Tm‐1	ToMV	Tobamovirus	184‐kDa protein	8	6	2 years	Broken down	Common	1	0.007	0.005	0.169	Meshi et al. (1988); Strasser and Pfitzner (2007)
Tomato	Tm‐2	ToMV	Tobamovirus	MP	11	6	2–3 years	Broken down	Common	1	0.005	0.006	0.314	Meshi et al. (1989); Strasser and Pfitzner (2007)
Pepper	L3	PMMoV	Tobamovirus	CP	18	6	5 years	Broken down	Common	1	0.029	0.020	0.204	Berzal‐Herranz et al. (1995); Hamada et al. (2007)
Sugar beet	Rz‐1	BNYVV	Benyvirus	P25	33	4	6–11 years	Broken down	Common	1	0.022	0.037	0.969	Acosta‐Leal and Rush (2007); Chiba et al. (2008)
Soybean	Rsv‐1	SMV	Potyvirus	P3‐HcPro	8	7	15 years	Broken down	Common	2	0.034	0.022	0.132	Eggenberger and Hill (1997); Eggenberger et al. (2008); Hajimorad et al. (2006)
Barley	rym‐4	BaYMV	Bymovirus	VPg	15	4	>20 years	Broken down	Common	2	0.053	0.050	0.258	Kühne et al. (2003)
Pepper	pvr21	PVY	Potyvirus	VPg	11	6	>20 years	Broken down	Common	2	0.090	0.065	0.137	Moury et al. (2004)
Potato	Nb	PVX	Potyvirus	25‐kDa protein	9	4	>20 years	Broken down	Common	2	0.035	0.021	0.096	Malcuit et al. (1999)
Rapeseed	TuRB01	TuMV	Potyvirus	CI	29	9	>20 years	Broken down	Common	2	0.138	0.030	0.029	Jenner et al. (2000)
Pepper	pvr22	TEV	Potyvirus	VPg	15	7	>20 years	Broken down	Common	2	0.068	0.050	0.194	Kang et al. (2005a)
Rice	rymv‐1	RYMV	Sobemovirus	VPg	18	4	>20 years	Broken down	Common	2	0.076	0.031	0.075	Hébrard et al. (2006)
Tomato	Tm‐22	ToMV	Tobamovirus	MP	11	6	>20 years	Not broken down	Rare	3	0.005	0.006	0.314	Weber et al. (1993); Strasser and Pfitzner (2007)
Potato	Nx	PVX	Potexvirus	CP	26	4	>20 years	Not broken down	Rare	3	0.086	0.040	0.058	Santa Cruz and Baulcombe (1995)
Potato	Rx	PVX	Potexvirus	CP	26	4	>20 years	Not broken down	Rare	3	0.086	0.040	0.058	Bendahmane et al. (1995)
Pepper	pvr22	PVY	Potyvirus	VPg	11	6	>20 years	Not broken down	Rare	3	0.090	0.065	0.137	Moury et al. (2004)
Bean	wlv	BYMV	Potyvirus	VPg	10	8	>20 years	Not broken down	Rare	3	0.160	0.109	0.100	Bruun‐Rasmussen et al. (2007)
Potato	Ry	PVY	Potyvirus	Nia‐Pro	23	7	>20 years	Not broken down	Not reported	4	0.128	0.053	0.068	Mestre et al. (2000)
Tobacco	N	TMV	Tobamovirus	183 kDa protein	10	6	>20 years	Not broken down	Not reported	4	0.025	0.011	0.087	Padgett et al. (1997)
Pepper	L1	ToMV	Tobamovirus	CP	17	6	>20 years	Not broken down	Not reported	4	0.014	0.017	0.186	Dardick et al. (1999); Hamada et al. (2007)

^* Upper‐ and lower‐case initials indicate dominant and recessive resistances, respectively.

^† CI, cylindrical inclusion protein; CP, coat protein; MP, movement protein; Nia‐Pro, nuclear inclusion a protein; NSs, nonstructural S protein; P3‐HcPro, protein 3 and helper component protease; P25, 25‐kDa protein; VPg, genome‐linked viral protein.

^‡ Evolutionary potential overall risk defined by García‐Arenal and McDonald (2003) or from bibliographical data (see Supporting Information).

^§ Average pairwise p distance estimated with mega 3.1 software.

^¶ Nonsynonymous/synonymous substitution rate ratio estimated by the single‐likelihood ancestor counting (SLAC) method implemented in HyPhy software.

^** Selected references for avirulence gene identification and amino acid substitutions involved in the resistance breakdown (when these are known).

BaYMV, Barley yellow mosaic virus; BNYVV, Beet necrotic yellow vein virus; BYMV, Bean yellow mosaic virus; PMMoV, Pepper mild mottle virus; PVX, Potato virus X; PVY, Potato virus Y; RYMV, Rice yellow mottle virus; SMV, Soybean mosaic virus; TEV, Tobacco etch virus; TMV, Tobacco mosaic virus; ToMV, Tomato mosaic virus; TSWV, Tomato spotted wilt virus; TuMV, Turnip mosaic virus.