Comparative genome composition of two closely related biocontrol strains of Bacillus velezensis endophytes

Abstract

Comparative genomics was carried out between Bacillus velezensis KV10 and KV15 endophytes isolated from Elytropappus rhinocerotis. The nucleotides from the isolates were sequenced on an Illumina platform and assembled using SPAdes. Taxonomical identification was determined by a measure of evolutionary distance and codon-based phylogenetic trees. Sequence alignment against a representative isolate was assessed with Mauve, and a unique genomic region was determined through genome BLAST against a representative strain using GView. Protein family sorter and comparative pathway tools assigned to RASTtk4 were used to align the shared proteins between the isolates. antiSMASH was used to identify gene clusters for the bioactive secondary metabolites. Identification of mutant variants was determined through SNP calling using BWA-MEM to align the reads and FreeBayes for high-quality variants. B. velezensis KV10 and KV15 have genome sizes of 3,992,370 bp and 3,880,685 bp, and GC contents of 46.37 % and 46.49 %, respectively. There are identified genetic and evolutionary dissimilarities between the two endophytic isolates. Nineteen proteins with well-defined functions were found unique to KV10, while a total of thirty-two proteins were found unique to KV15. Missense or synonymouspoint mutations were observed at different loci in the KV10 genome; all affected codons are involved in the formation of polyketide synthase and general stress protein (YdbA and YdbB). The affected genes by point mutations in the KV15 are YeeF and FliK. Both strains contain gene clusters putative for biosynthesis of specific antimicrobial metabolites such as difficidin, macrolactin, fengycin, bacillibactin, bacillaene, and bacilysin. While only KV10 has additional gene clusters for mersacidin and surfactin biosynthesis. In addition, biosynthetic metabolites extracted from both strains exhibited notable antimicrobial effectiveness against test Serratia marcescens and Fusarium sp. Both isolates exhibit putative genetic features and are supported by in vitro assessment as promising candidates for biocontrol agents.