Fig. 1 Antagonism of strain XDY66 against Botrytis cinerea，Phytophthora capsici and Fusarium oxysporum

Fig. 2 Botrytis cinerea’s mycelia deformity and top enlargement in PDA liquid medium supplemented with XDY66（arrow）

Fig. 3 The incidence of tomato fruits inoculated with Botrytis cinerea and strain XDY66

Fig. 4 Gram staining（A）and spore staining（B）of strain XDY66

Fig. 5 Phylogenetic tree of strain XDY66 and similar strains based on 16S rDNA

Fig. 6 Circular genome map of Bacillus velezensis XDY66 The first and fourth circles from the outside to the inside are CDS on the positive and negative chains，and different colors represent different COG functional classifications；The second and third circles are CDS，tRNA and rRNA on the positive and negative chains，respectively. The fifth circle is the GC content. The outward or inward direction indicates that the GC content in this region is higher or lower than the average content of the whole genome，and the higher the peak value indicates the greater the difference from the average content. The sixth circle is the GC-Skew value，and the specific algorithm is G-C/G+C，which can assist in judging the leading chain and the lagging chain.

Fig. 7 Homologous cluster（COG）analysis of Bacillus velezensis XDY66 A-Z are shown in Fig. 6.

Fig. 8 Genome comparison of Bacillus velezensis XDY66 with B. velezensis FZB42 and B. velezensis SQR9 Boxes with the same color are represented the syntenic regions，rearrangements are shown by colored lines.

Fig. 9 Venn figure，number of common and endemic homologous CDS genes of Bacillus velezensis XDY66，B. velezensis FZB42 and B. velezensis SQR9

Fig. 10 Collinearity analysis of secondary metabolite gene clusters of Bacillus velezensis XDY66，FZB42 and SQR9 Colinear regions are connected by black lines 1-14 are the corresponding secondary metabolite gene clusters. 1：Surfactin；2：LAP；3：Polyketide Synthase-Like；4：Terpene；5：Lanthipeptide-class-ii；6：Macrolactin H；7：Bacillaene；8：Fengycin；9：Terpene；10：Type III Polyketide Synthases；11：Difficidin；12：Bacillibactin；13：Bacilysin；14：Terpene.