Complete genome sequence of Bacillus subtilis SG6 antagonistic against Fusarium graminearum

•We present the whole genome of Bacillus subtilis SG6.•B. subtilis SG6 displays a strong F. graminearum inhibitory activity.•Six gene clusters devoted to synthesis of antimicrobial peptides and polyketides. Bacillus subtilis SG6 exhibited a high antifungal effect on the mycelium growth, sporulation and DON production of F. graminearum and significantly reduced disease incidence, Fusarium head blight (FHB) index and DON in the field. Here, we present the complete genome sequence of B. subtilis SG6, providing insights into the genomic basis of its effects and facilitating its application in FHB control.