Whole-Genome Sequencing and Analysis Reveals Plant Growth-Promoting Properties and Biocontrol Potential of the Crotalaria retusa Endophytic Bacillus velezensis Strain G2T39

<i>Bacillus velezensis</i> strain G2T39 is an endophytic bacterium previously isolated from <i>Crotalaria retusa</i> L., with evidenced biocontrol activity against <i>Fusarium oxysporum</i> f. sp. <i>Cubense</i> and <i>Fusarium graminearum</i>. In this study, it was shown that this strain also exhibited biocontrol activity against <i>Colletotrichum gloeosporioides</i> and <i>Fusarium oxysporum</i> f. sp. Vasinfectum, two important crop pathogens in tropical zones. Comprehensive phylogenetic and genomic analyses were performed to further characterize this strain. The genome of <i>B. velezensis</i> G2T39 consists of a single circular chromosome of 4,040,830 base pairs, with an average guanine-cytosine (GC) content of 46.35%. Both whole-genome-based phylogeny and average nucleotide identity (ANI) confirmed its identity as <i>B. velezensis</i>, being closely related to biocontrol and plant growth promotion Gram-positive model strains such as <i>B. velezensis</i> FZB42. Whole-genome annotation revealed 216 carbohydrate-active enzymes and 14 gene clusters responsible for secondary metabolite production, including surfactin, macrolactin, bacillaene, fengycin, bacillibactin, bacilysin, and difficidin. Genes involved in plant defense mechanisms were also identified. Additionally, G2T39 genome harbors multiple plant growth-promoting traits, such as genes associated with nitrogen metabolism (<i>nifU</i>, <i>nifS</i>, <i>nifB</i>, <i>fixB</i>, <i>glnK</i>) and a putative phosphate metabolism system (<i>phyC</i>, <i>pst glpQA</i>, <i>ugpB</i>, <i>ugpC</i>). Additional genes linked to biofilm formation, zinc solubilization, stress tolerance, siderophore production and regulation, nitrate reduction, riboflavin and nicotinamide synthesis, lactate metabolism, and homeostasis of potassium and magnesium were also identified. These findings highlight the genetic basis underlying the biocontrol capacity and plant growth-promoting properties of <i>B. velezensis</i> G2T39 and support its potential application as a sustainable bioinoculant in agriculture.