RXLR effector genes mediate regional adaptation of Phytophthora infestans

Abstract

Local adaptation has been a central theme of eco-evolutionary research for decades. It is generally assumed that plant pathogens are locally adapted due to their standing interactions with biotic and abiotic factors in the ecosystem. Effectors, secreted small proteins encoded by pathogens, play critical roles in host–pathogen interactions, by activating host genotype-specific resistance, suppressing plant immunity, and playing other functions. In this study, we investigated the potential involvement of RXLR effector genes in ecological adaptation by examining the simple sequence repeat (SSR), virulence, and effector profiles in Phytophthora infestans isolates collected from two geographic regions differing in ecological environments. Genotypic analyses with SSR markers and virulence assays showed that the pathogen from the two regions shared genetic background but differed in virulence spectrums. High-throughput sequencing and expression analysis of 24 selected P. infestans isolates further showed variations in the RXLR effector repertoire, ranging from 536 to 548 for each isolate and the expression of effector genes was highly associated with the accumulation of homologous sRNA. Regional specific alleles were detected at 94 RXLR effector genes, and a specific accumulation of homologous 25–26 nt sRNAs was found at 67 RXLR effector genes. Two of the regional specific RXLR effector genes were confirmed to be virulence factors. Taken together, these results suggest that genomic and epigenetic variations in RXLR effector genes contribute significantly to the ecological adaptation of P. infestans populations and that regional specific effector genes will help to understand the adaptive landscape of pathogens and efficient use of host resistance genes.