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Background Paris polyphylla  is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of  P. polyphylla  in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on  P. polyphylla  are valuable and urgently needed. Results In this paper, we reported the biocontrol efficiency of  Paenibacillus peoriae  HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on  P. polyphylla  in the greenhouse and field .  The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to  P. peoriae  IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified .  Conclusions This study revealed that  P. peoriae  HJ-2 could serve as a potential BCA against stem rot on  P. polyphylla . Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism