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Bacillus amyloliquefaciens  is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of  B. amyloliquefaciens  using comparative genomics analysis. All the available 96 genomes of  B. amyloliquefaciens  strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that  B. amyloliquefaciens  is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the  B. amyloliquefaciens  genome. The majority of plant-associated strains of  B. amyloliquefaciens  were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes  tmrB  and  yuaB  codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while  clpP , which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of  B. amyloliquefaciens  reflects their adaption to different niches.

frontiers in genetics

Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes