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The  Bacillus velezensis  strain PG12, belonging to the  Bacillus amyloliquefaciens  group, is an endophytic bacterium known for its antimicrobial activities against crop pathogens. However, our knowledge of the molecular basis underlying its biocontrol activity and the relatedness of different strains in the  Bacillus amyloliquefaciens  group is limited. Here, we sequenced and analyzed the genome of PG12 to test its taxonomic affiliation and identified genes involved in the biocontrol activity. The phylogenomic analysis results indicate that PG12 belongs to  B. velezensis,  a subgroup of the  B. amyloliquefaciens  group. By comparing the genomes of 22 strains in this group, we confirmed that it comprises three different phylogenetic lineages:  B. amyloliquefaciens ,  B. velezensis  and  B. siamensis . Three secondary metabolism gene clusters related to the production of lipopeptides, namely fengycin, iturin and surfactin, were identified in the genomes of the  B. amyloliquefaciens  group. The core genome of  B. velezensis  is enriched in secondary metabolism genes compared with  B. siamensis  and  B. amyloliquefaciens . Three of the five genes pertaining to the gene cluster responsible for fengycin biosynthesis ( fenBCD ) were found in  B. velezensis  and  B. siamensis , but not in  B. amyloliquefaciens . Phenotypic analysis showed that the ∆ fenA  mutant of PG12 displayed significantly decreased biofilm formation and swarming motility, which indicates that fengycin contributes to the colonization and pathogen control abilities of PG12. Our results also suggest that  B. siamensis  and  B. velezensis  have acquired the  fenBCD  genes from  Paenibacillus  spp. by horizontal gene transfer (HGT). Taken together, the results provide insights into the evolutionary pattern of the  B. amyloliquefaciens  group strains and will promote further researches on their taxonomy and functional genomics.

Organization, evolution and function of fengycin biosynthesis gene clusters in the Bacillus amyloliquefaciens group