Abstract: Paenibacillus polymyxa T-9 exhibits a strong inhibitory effect against plant pathogens like Fusarium oxysporum f. sp. cucumerinum. In this study, whole-genome sequencing of the T-9 strain was conducted using a combination of second-generation BGISEQ and third-generation PacBio platform to determine its underlying antibacterial mechanism. The sequencing data were subjected to genome assembly, gene prediction and functional annotation, collinearity analysis, secondary metabolite synthesis gene cluster prediction, and comparative genome analysis. The results showed that the strain T-9 was composed of a 5621664-bp genome, with a 45.52% GC content. It encoded 4937 open reading frames (ORFs), including 109 tRNA genes, 42 rRNA, 0 sRNA, 6 tandem repeat sequences, and 5 satellite RNAs. Additionally, 4888, 3603, 4422, 3512, and 2261 genes were annotated in the NR, Swiss Prot, eggNOG, GO, and KEGG databases, respectively. Moreover, 18 secondary metabolite gene clusters were predicted in the T-9 strain, of which 6 showed 100% similarity namely fusaricidin B, paenibacillin, tridecaptin M, thermoactinamide A, polymyxin, and paenicidin A. Among these antibiotic synthesis gene clusters, paenibacillin and tridecaptin M were unique to the strain T-9. Comparative genomic analysis was conducted with Paenibacillus polymyxa CR1, M1, HY96-2, SC2, and SQR-2, which exhibit biocontrol function. The results revealed that the strain T-9 streamlined some genes during evolution, with nine specific gene clusters, including two genes encoding cholinergic toxin (Hol-Tox) and tryptophan RNA binding decay protein (MtrB). This paper provides a preliminary analysis of the antibacterial mechanism of the strain T-9 at the genetic level, providing reference information for a more comprehensive understanding of the secondary metabolite synthesis pathways in Paenibacillus polymyxa and subsequent research on the strain T-9.

Key words: Paenibacillus polymyxa, genome, gene annotation, secondary metabolism