Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria

•We present the whole genome sequence of Bacillus velezensis LS69.•B. velezensis LS69 shows a strong antagonistic activity against a variety of pathogenic bacteria.•3Genome analysis identified ten gene clusters involved in nonribosomal synthesis of polyketides, cyclic lipopeptides and bacteriocins.•B. velezensis LS69 harbors a series of genes involved in enhancing plant growth and triggering plant immunity. Bacillus velezensis LS69 was found to exhibit antagonistic activity against a diverse spectrum of pathogenic bacteria. It has one circular chromosome of 3,917,761bp with 3,643 open reading frames. Genome analysis identified ten gene clusters involved in nonribosomal synthesis of polyketides (macrolactin, bacillaene and difficidin), lipopeptides (surfactin, fengycin, bacilysin and iturin A) and bacteriocins (amylolysin and amylocyclicin). In addition, B. velezensis LS69 was found to contain a series of genes involved in enhancing plant growth and triggering plant immunity. Whole genome sequencing of Bacillus velezensis LS69 will provide a basis for elucidation of its biocontrol mechanisms and facilitate its applications in the future.