show Abstracthide AbstractBacillus subtilis is the focus of both academic and industrial research. Previous studies have reported a number of differences between environmental and domesticated laboratory strains of B. subtilis. To uncover the genetic variation between environmental and laboratory strains, we performed whole genome sequencing of two environmental B. subtilis isolates, KM and CGMCC63528, and compared their genomes with that of laboratory strain 168. We found significant sequence differences between the two environmental B. subtilis strains and 168, including more than 20,000 single nucleotide polymorphism (SNPs) for each strain. Of these, 9323 SNPs in more than 2000 genes were common to the two environmental strains. The missense changes were significantly correlated between KM and CGMCC63528, and one third of the top 100 most significantly altered genes were identical between these two isolates. Transformation-related genes, including genes in the comG operons, comC, comEC and nucA, were significantly altered in environmental strains. These results provide a framework for further comparative genetic analyses of environmental and laboratory B. subtilis strains, including differences in transformation-competence-specific genes, which would aid in developing the transformability of environmental B. subtilis strains.