A conserved small RNA-generating gene cluster undergoes sequence diversification and contributes to plant immunity

Small RNA-mediated gene silencing has emerged as an integral component of plant immune system. The secondary small interfering RNA (siRNAs) pathway contributes to defense by silencing target genes in invading fungal and oomycete pathogens. A major source of secondary siRNAs is transcripts potentially encoding pentatricopeptide repeat (PPR) proteins. Here, we report that siRNA production is an ancient function of an evolutionarily conserved clade of PPR genes that undergo remarkable within-species diversification. In Arabidopsis thaliana, the siRNA-spawning PPRs are physically clustered in one locus on Chromosome 1. These sequences are diversified through gene duplication followed by sequence diversification as well as accumulation of high-impact variations including pseudogenization. This diversity leads to the accumulation of a diverse PPR-siRNA pool, consistent with an engagement in a co-evolutionary arms race with the pathogens. This study defines siRNA-producing PPRs as a family of defense genes and highlights PPR-siRNA-based engineering for enhancing broad-spectrum disease resistance.