Fungi Verticillium are plant pathogens that cause disease in a large number of hosts. Natural resistance to race 1 strains of V. dahliae was found in tomato Solanum lycopersicum (gene Ve1) and to race 2 strains in tomato Solanum neorickii (gene V2). The fungal effectors recognized by these two genes were not discovered until 2012 (Ave1) and 2020 (Av2). The methods used to identify effectors were DNA sequencing, comparative genomics, transcriptomics, functional analyses by co-expression, transformation, and gene deletion. Based on genome sequence data, phylogenetic studies have also been done to identify the evolutionary origin of genes for effectors. Ave1 was identified by comparing several genomes of V. dahliae strains of race 1 and race 2 and focused on parts of the genome that are common to all strains of race 1 and absent in all strains of race 2. Transcriptomics were used to determine which genes within this region of the genome are expressed during the infection of the plant and then targeted gene deletion was used to confirm that it is indeed the recognition of Ave1 gene by Ve1 that triggers resistance. Identification of Av2 was performed according to two scenarios, as it was not known whether race 1 strains contained this gene or not. They compared the genomes of race 1 and 2 strains with race 3 genomes that do not have the Av2 gene. Thus, candidate genes were determined and then, by gene expression and deletion, they identified which gene is V2.
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