In order to establish a successful infection, fungal plant pathogens must invade the host plant and overcome host defences, either by suppressing or counteracting them. Pathogenesis defines “the cycle of disease progression in the host from initial infection to onset of symptoms” (Lucas, 1998). The fungal genes necessary for pathogenesis are described in multiple ways. Idnurm and Howlett (2001) have broadly defined pathogenicity genes as “genes required for the development of diseases, but are not needed for a pathogen to complete their life cycle.”
Complex mechanisms have formed by pathogenic fungi to defeat plant immune systems over long periods of co-evolution. A subset of pathogenic genes called effectors is described as small proteins secreted by a wide range of plant pathogen including fungi, bacteria and nematodes that function within the host plant cells to modify the host cellular structure, promote infections and suppress plant immunity reactions. Effectors can promote the lifestyle of the pathogen and determine the level of specificity of the host. Such proteins are usually rich in cysteine and lack homologues in closely related species (Van de Wouw and Howlett 2011). Several of these effectors can acting as avirulence and virulence factors by triggering the defensive response of the host or suppressing basal immunity (Kamoun, 2006, 2007; Hogenhout et al., 2009; Lo Presti et al., 2015). These factors can be recognised by the host plant and lead to plant resistance. Casadevall and Pirofski (1999) described virulence as “relative potential to cause damage to the host”. Standard criteria used to classify fungal effector proteins are the small sizes (i.e. less than 300 amino acids in length), existence of signal peptide regions, and several cysteine residues. However, the absence of overlapping genes, gene duplication, extensive diversification of genome, and other genetic re-arrangements, such as recombination of novel protein domains, indicate complex phylogenetic origins (Stergiopoulos and De Wit, 2012). Therefore, it was hard to find similar features in effector sequences which would require a more reliable classification as a group or protein family (Stergiopoulos and de Wit, 2009; Lo Presti et al., 2015; Guillen et al., 2015). As a phytopathogenic fungus, F.oxysporum uses effector proteins that are secreted during the colonization of the host to produce infection. These include proteins that target plant physical or chemical barriers such as the previously mentioned small cysteine-rich proteins i.e. the majority of SIX proteins, cell wall degrading enzymes, and necrosis-inducing proteins, among others (Di Pietro et al., 2003; van der Does and Rep, 2007; Michielse and Rep, 2009; de Sain and Rep, 2015).