Deletions, repeat-induced point mutations and amino acid substitutions drive evolution of linked effectors in a fungal plant pathogen

Abstract

Pathogen effectors, molecules that include small secreted proteins such as avirulence proteins, facilitate infection or induce defence responses by plants. We report the first large scale study of evolutionary processes affecting linked effector-like genes in a fungal plant pathogen. Mutations affecting seven genes and four single copy non-coding regions located in a 520 kb repetitive element-rich region of Leptosphaeria maculans, a pathogen of Brassica napus (canola) are described. Two genes are avirulence genes, AvrLm1 and AvrLm6, which are complementary to B. napus resistance genes, Rlm1 and Rlm6. Analyses of 295 Australian isolates showed that deletions, Repeat-Induced Point (RIP) mutations and/or non-RIP derived amino acid substitutions account for rapid evolution of four small secreted proteins. RIP was confined to three genes and two other single copy regions and appeared to have ‘leaked’ from flanking repetitive sequences. The RIP alleles were monophyletic and present only in isolates collected after 2004, the year when canola cultivars with resistance conferred by Rlm1 suffered severe yield losses. This co-incided with a large increase in the frequency of isolates with virulence alleles of AvrLm1 and AvrLm6, even though the canola cultivars lacked Rlm6. Evolution of these two effectors thus appears to be influenced both by the genomic environment (flanking repetitive elements) and by selection pressure from extensive sowing of crop varieties with resistance genes complementary to the avirulence effector gene