Evidence of extensive positive selection acting on cherry (Prunus avium L.) resistance gene analogs (RGAs)

Abstract

The cherry tree (Prunus avium L.), is an important tree species which is intensively plagued by many phytopathogenic fungal species. Resistance gene analogs (RGAs) are the largest class of resistance (R) genes and are pivotal components at breeding projects, serving as useful functional markers linked to R genes. In order to assess the evolutionary pressures acting upon P. avium RGAs candidates, their 173 homologues that have previously been deposited in GenBank were mined. Their proteins were clustered according to their blast(p) similarities in 12 MCL (Markov Cluster Algorithm) tribes, resulting in unique and well supported paralogous gene groups (PGGs). The extent to which these genes exhibit evidence of adaptive, positive selective pressures, which are causing excessive fixation of non-synonymous mutations, was determined using a series of maximum likelihood analyses using the PAML package. The results postulate existence of robust evidence of positive selection, acting in almost all of the clustered PGGs across their phylogenies. Furthermore, analyses revealed that the majority of the positively selected amino acid residues sites are localized widely across these RGAs sequences. We speculate that the clustered distribution of these RGAs might also be pronounced of high birth and death genes rates with diversifying episodes acting on their NB-ARC domains, putatively affecting their ligandbinding specificities. Such evolutionary insights shed light on how these NBS-encoding RGAs in P. avium are being evolved, assigning them as the foremost surveillance mechanism against rapidly evolving fungal pathogens, and providing breeders with effective tools for fast-tracking the development of varieties with more durable resistance.