Comparative genomics and transcriptomics identify Rhizoctonia solani AG-7 cytochrome P450 gene RsCYP-1 for pencycuron resistance

<i>Rhizoctonia solani</i> is a destructive fungal pathogen that causes major crop losses worldwide. The fungicide pencycuron is commonly used to control Rhizoctonia diseases, but some <i>R. solani</i> anastomosis groups (AGs) such as AG-7 are generally resistant to pencycuron. This study discovered a sensitive AG-7 isolate (No.214), and compared its genomics and transcriptomics to a resistant isolate (No.213). PacBio whole-genome sequencing and Illumina RNA sequencing (RNA-seq) revealed that No.214 has a whole-genome duplicated and pentaploid genome, showed broad transcriptional changes but lacked key detoxification genes in response to pencycuron. In contrast, No. 213 has a diploid genome and the transcriptional responses were mostly xenobiotic detoxification genes such as cytochrome P450 (<i>RsCYP-1</i>). Functional validation in <i>Monilinia fructicola</i> confirmed <i>RsCYP-1</i> conferred pencycuron resistance. Collectively, this work advances the understanding of cytochrome P450-mediated pencycuron resistance and suggests genomic complexity of <i>R. solani</i> AG-7 isolates may influence pencycuron susceptibility.