Transposable elements impact the population divergence of rice blast fungus .

Unlabelled: Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In , genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in population evolution and divergence, our understanding of TEs in this context remains limited. Here, we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in populations. Our results show that these TEs have specifically expanded in recently isolated rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/ and Xian/ rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the rice-infecting lineage.

Importance: is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward the two rice subspecies, Xian/ and Geng/. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of remain largely unknown. In this study, we reported that TEs shape the population divergence of by differentially regulating gene expression between Xian/-infecting and Geng/-infecting populations. Our results revealed a TE insertion-mediated gene expression adaption that led to the divergence of population infecting different rice subspecies.