Genome sequencing and experimental validation reveal the biocontrol activity of endophytic Bacillus velezensis XY3 against Colletotrichum fructicola

• XY3 inhibits conidial germination and hyphae growth of C. fructicola . • The EC 50 value of crude lipopeptides derived from XY3 was 21.33 μg/mL. • IturinA, fengycinA and surfactin of XY3 were examined by LC-MS/MS analysis. • IturinA and fengycinA showed antifungal activity against C. fructicola . Tea anthracnose, caused by Colletotrichum spp., is a prevalent foliar disease in the primary tea-planting regions of China. The conventional chemical control of tea anthracnose results in excessive fungicide residues, which constrain the export of tea from our country. Therefore, it is imperative to develop safe and pollution-free biological control methods. Strain XY3, isolated from the healthy leaves of ‘Xinyang 10’ cultivar and identified as Bacillus velezensis through 16S rRNA gene analysis, demonstrated significant inhibition of conidial germination, hyphal growth, and the pathogenicity of Colletotrichum fructicola . Propidium iodide and Hoechst staining assays indicated that the membrane permeability of the mycelium was compromised when cultured with the fermentation broth of XY3. Crude lipopeptides were extracted from fermentation broth showing an EC 50 value of 21.33 µg mL −1 , and the antimicrobial compounds including iturinA, fengycinA, surfactin, and their homologs were detected via LC-MS/MS. Plate confrontation assay verified that iturin and fengycin purified compounds exhibited notable inhibitory activities. Additionally, the whole genome of XY3 was sequenced with 46.5 % GC content in the size of 3.93 Mb circular chromosome. Subsequent, Go, KEGG and COG analysis were conducted, identifying 102 carbohydrate-active enzymes, 12 gene clusters of secondary metabolites. Comparative genomic analysis revealed that two unique genes ctg_01263 and ctg_01267 of strain XY3 are related to lanthipeptide synthetase synthesis. These functional analyses reveal a numerous genes involved in the biosynthesis of antagonistic metabolites antagonistic to pathogens. Besides, XY3 also exhibits the potential in promoting plant growth by producing indole-3-acetic acid. Collectively, B. velezensis XY3 emerges as a promising biocontrol agent against C. fructicola .