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Background  Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons can become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity.    Results  We uncover a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. The aggressive fungal plant pathogen,  Botrytis cinerea , is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs ( Bc sRNAs) into plant cells to suppress host gene expression for infection. We find that naturally occurring, less aggressive  B. cinerea  strains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposon  Bc sRNA production. Using a transgenic proof-of-concept approach, we reconstitute retrotransposon expression in a  Bc sRNA-lacking  B. cinerea  strain, which results in enhanced aggressiveness in a retrotransposon and  Bc sRNA expression-dependent manner. Moreover, retrotransposon expression in  B. cinerea  leads to suppression of plant defence-related genes during infection.    Conclusions  We propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-species  Bc sRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have a broad impact on studies of host-microbe interactions and pathology.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13059-021-02446-4.

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea