Evidence for intragenic recombination and selective sweep in an effector gene of Phytophthora infestans

Abstract

Effectors, a group of small proteins secreted by pathogens, play a critical role in the antagonistic interaction between plant hosts and pathogens through their dual functions in regulating host immune systems and pathogen infection capability. In this study, evolution in effector genes was investigated through population genetic analysis of Avr3a sequences generated from 96 Phytophthora infestans isolates collected from six locations representing a range of thermal variation and cropping systems in China. We found high genetic variation in the Avr3a gene resulting from diverse mechanisms extending beyond point mutations, frameshift, and defeated start and stop codons to intragenic recombination. A total of 51 nucleotide haplotypes encoding 38 amino acid isoforms were detected in the 96 full sequences with nucleotide diversity in the pathogen populations ranging from 0.007 to 0.023 (mean = 0.017). Although haplotype and nucleotide diversity were high, the effector gene was dominated by only three haplotypes. Evidence for a selective sweep was provided by (i) the population genetic differentiation (G_ST) of haplotypes being lower than the population differentiation (F_ST) of SSR marker loci; and (ii) negative values of Tajima's D and Fu's FS. Annual mean temperature in the collection sites was negatively correlated with the frequency of the virulent form (Avr3a^EM), indicating Avr3a may be regulated by temperature. These results suggest that elevated air temperature due to global warming may hamper the development of pathogenicity traits in P. infestans and further study under confined thermal regimes may be required to confirm the hypothesis.

Keywords: Phytophthora infestans; climate change; compensatory mutation; effector genes; evolution; recombination; selective sweep; temperature dependent.

Figure 1

Frequency and spatial distribution of Avr3a haplotypes in the Phytophthora infestans isolates sampled from six geographical locations in China

Figure 2

Mechanisms of generating genetic variation in Avr3a gene of Phytophthora infestans: (a) DNA sequences showing point mutations, early termination, single base deletion, and defeated start and stop codons in Avr3a. Point mutations in start and stop codons are highlighted with bold letters, and the single base deletions are highlighted with bold dash lines; (b) intragenic recombinant generated by YN3, an Avr3a^EM form, and YN8, an isoform in Clade 3

Figure 3

Phylogenetic relationship and haplotype network in the Avr3a sequences generated from 96 Phytophthora infestans isolates collected from six geographical locations in China; (a) phylogenetic relationships among the 51 Avr3a nucleotide haplotypes of P. infestans reconstructed by a Bayesian inference. Posterior probability of topology was generated by 1,000,000 bootstrapping and is shown on the three main clusters. The most common (H‐1, H‐3, and H‐10) and the recombinant (H46) sequences were highlighted with bold letters; (b) haplotype network of 51 Avr3a nucleotide sequences and circle sizes of the circles represent haplotype frequencies in populations

Figure 4

Correlation between annual mean temperature in collection sites and the frequency of Avr3a^EM