Intragenic Recombination and Positive Selection Contribute to High Allelic Diversity in Effector Genes of the Banana Pathogen Mycosphaerella fijiensis

We have recently showed that functional homologs of the Avr4 and Ecp2 effectors from the tomato pathogen Cladosporium fulvum are present in the phylogenetically related banana pathogen Mycoshpaherella fijiensis. Such homologous effectors are collectively recognized by the cognate Cf-4 and putative Cf-Ecp2 resistance proteins from tomato, which could thus mediate resistance against M. fijiensis if genetically transformed and functional in the genetic background of plantain (Musa spp.) However, disease resistance controlled by single dominant genes could be overcome by mutated alleles of effectors that are no longer recognized by the cognate resistance proteins. Here, we surveyed the existing allelic variation in the MfAvr4, MfEcp2-1, MfEcp2-2 and MfEcp2-3 effectors from 34 M. fijiensis strains collected from major banana-growing areas around the world and assayed its impact on recognition by the cognate tomato resistance proteins. Overall nucleotide sequence divergence was highest for MfEcp2-3, followed by MfAvr4, MfEcp2 and finally MfEcp2-2. Most allelic variation is present in strains originating from SE Asia, which is also the center of origin of Musa spp., and thus might represent adaptation to different Musa genotypes and/or ancient balanced polymorphisms. A large number of synonymous and non-synonymous substitutions were identified in all four effector genes, while tests of neutrality indicated a deviation from the neutral theory of molecular evolution. Positive diversifying selection was detected, while in MfEcp2-3 adaptive evolution was strongly associated with intragenic recombination. High diversification in effectors of M. fijiensis may reveal co-evolution with cognate resistance proteins in plantain or other effector targets.