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Background  Anastomosis group 1 IA (AG1-IA) of  Rhizoctonia solani  is the major agent of banded leaf and sheath blight (BLSB) disease that causes severe yield loss in many worldwide crops. MicroRNAs (miRNAs) are ~ 22 nt non-coding RNAs that negatively regulate gene expression levels by mRNA degradation or translation inhibition. A better understanding of miRNA function during AG1-IA infection can expedite to elucidate the molecular mechanisms of fungi-host interactions.    Results  In this study, we sequenced three small RNA libraries obtained from the mycelium of AG1-IA isolate, non-infected maize sheath and mixed maize sheath 3 days after inoculation. In total, 137 conserved and 34 novel microRNA-like small RNAs (milRNAs) were identified from the pathogen. Among these, one novel and 17 conserved milRNAs were identified as potential virulence-associated (VA) milRNAs. Subsequently, the prediction of target genes for these milRNAs was performed in both AG1-IA and maize, while functional annotation of these targets suggested a link to pathogenesis-related biological processes. Further, expression patterns of these virulence-associated milRNAs demonstrated that theyparticipate in the virulence of AG1-IA. Finally, regulation of one maize targeting gene,  GRMZM2G412674  for Rhi-milRNA-9829-5p, was validated by dual-luciferase assay and identified to play a positive role in BLSB resistance in two maize mutants. These results suggest the global differentially expressed milRNAs of  R. solani  AG1-IA that participate in the regulation of target genes in both AG1-IA and maize to reinforce its pathogenicity.    Conclusions  Our data have provided a comprehensive overview of the VA-milRNAs of  R. solani  and identified that they are probably the virulence factors by directly interfered in host targeting genes. These results offer new insights on the molecular mechanisms of  R.solani -maize interactions during the process of infection.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02930-w.

Identification of virulence associated milRNAs and their bidirectional targets in Rhizoctonia solani and maize during infection