IntroductionSugarcane is one of the most important sugar crops worldwide, however, sugarcane production is seriously limited by sugarcane red rot, a soil-borne disease caused byColletotrichum falcatum.Bacillus velezensisYC89 was isolated from sugarcane leaves and can significantly inhibited red rot disease caused byC. falcatum.MethodsIn this study, the genome of YC89 strain was sequenced, its genome structure and function were analyzed using various bioinformatics software, and its genome was compared with those of other homologous strains. In addition, the effectiveness of YC89 against sugarcane red rot and the evaluation of sugarcane plant growth promotion were also investigated by pot experiments.ResultsHere, we present the complete genome sequence of YC89, which consists of a 3.95 Mb circular chromosome with an average GC content of 46.62%. The phylogenetic tree indicated that YC89 is closely related toB. velezensisGS-1. Comparative genome analysis of YC89 with other published strains (B. velezensisFZB42,B. velezensisCC09,B. velezensisSQR9,B. velezensisGS-1, andB. amyloliquefaciensDSM7) revealed that the strains had a part common coding sequences (CDS) in whereas 42 coding were unique of strain YC89. Whole-genome sequencing revealed 547 carbohydrate-active enzymes and identified 12 gene clusters encoding secondary metabolites. Additionally, functional analysis of the genome revealed numerous gene/gene clusters involved in plant growth promotion, antibiotic resistance, and resistance inducer synthesis.In vitropot tests indicated that YC89 strain controlled sugarcane red rot and promoted the growth of sugarcane plants. Additionally, it increased the activity of enzymes involved in plant defense, such as superoxide dismutase, peroxidase, polyphenol oxidase, chitinase, and β-1,3-glucanase.DiscussionThese findings will be helpful for further studies on the mechanisms of plant growth promotion and biocontrol byB. velezensisand provide an effective strategy for controlling red rot in sugarcane plants.