Abstract:Through processes such as average nucleotide identity analysis，gene prediction，pan-genome construction，and functional annotation，the genome of 66 strains of Bacillus amyloliquefaciens was subjected to pan-genome analysis.The average nucleotide identity analysis showed that the above strains could be divided into two distinct branches with clear species boundaries.The obtained pan-genome contained 13 051 genes，including 2 165 core genes.Carbohydrate-active enzymes（CAZy）functional annotation showed that B.amyloliquefaciens had significant advantages over other Bacillus species in the degradation of starch，β-glucan，and xylan.Regarding plant growth promotion，B.amyloliquefaciens synthesized indole-3-acetic acid through the indole-3-pyruvic acid pathway and utilized alkaline phosphatase and phytase to release phosphorus.Antibiotic resistance analysis revealed the presence of genes conferring resistance to streptomycin and macrolide antibiotics in most strains.Additionally，secondary metabolite gene clusters such as baculene and bacitracin were identified in all genomes.This study further elucidated the taxonomic characteristics and core metabolic features of the B.amyloliquefaciens genome，as well as the advantages and potential of strains in carbohydrate metabolism，plant growth promotion，and biocontrol.These findings can serve as a reference for the better development and utilization of this bacterium.