Genome and transcriptome analysis of Chinese wheat powdery mildew isolate 21–2 for discovery of important virulence determinants

Wheat powdery mildew caused by Blumeria graminis f. sp tritici (Bgt), an obligate biotrophic fungal pathogen, is a destructive disease world-wide, particularly severe in China. However, the molecular mechanisms underlying virulence variation and pathogenesis of Chinese Bgt isolates remain poorly understood. Here, we constructed a chromosome-level genome assembly (136.19 Mb) of Chinese isolate 21–2, with repetitive element expansion (predominantly retrotransposons), by integrating Illumina, PacBio, Nanopore, and Hi-C sequencing technologies. The genome was predicted to contain 9215 protein-coding genes, of which 1569 were assessed as pathogenicity-related genes. This included 998 effectors, 371 involved in pathogen-host interactions (PHI), 223 CAZymes-encoding with plant cell wall degrading capacity, and 79 lipase-coding implicated in pathogenic infection. Compared to Swiss isolate 96224, isolate 21–2 displayed a distinct virulence pattern on 21 wheat differential lines. Comparative genomics analysis revealed that variations in composition and sequence of effector genes between the two isolates resulted in different virulence spectra (e.g., AvrPm1a, AvrPm3^a2/f2, AvrPm3^b2/c2, AvrPm3^d3). Transcriptome analysis of 21–2 revealed 64 effector genes exhibiting preferential expression during haustorial development, suggesting their potential involvement in pathogenesis. Among them, one can bind a defence-related protein of wheat and may play a key role in suppressing host immune responses and promoting disease progression. This study provides comprehensive genomic and transcriptomic insights into Chinese Bgt isolate 21–2, and reveals virulence determinants and their variants fundamental to pathogenesis. Future functional analysis of such genes will enhance our understanding of pathogenic mechanisms of powdery mildews.