Complete genome sequence of the biocontrol agent Bacillus velezensis UFLA258 and its comparison with related species: Diversity within the commons

Authors: DE JESUS SILVA, FABIOLA - Federal University Of Lavras; CARVALHO FERREIRA, LARISSA - Aberystwyth University; CAMPOS, VICENTE - Federal University Of Lavras; CRUZ-MAGALHAES, VALTER - Federal University Of Lavras; BARROS, ALINE - Federal University Of Lavras; ANDRADE, JACKELINE - Universidade Feira De Santana; Roberts, Daniel; DE SOUZA, JORGE - Federal University Of Lavras

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2019
Publication Date: 10/3/2019
Citation: De Jesus Silva, F., Carvalho Ferreira, L., Campos, V.P., Cruz-Magalhaes, V., Barros, A.F., Andrade, J.P., Roberts, D.P., De Souza, J.T. 2019. Complete genome sequence of the biocontrol agent Bacillus velezensis UFLA258 and its comparison with related species: Diversity within the commons. Genome Biology and Evolution. 11(10):2818-2823. https://doi.org/10.1093/gbe/evz208.
DOI: https://doi.org/10.1093/gbe/evz208

Interpretive Summary: Biological control agents are needed for control of plant pathogens due to environmental problems associated with some chemical controls and the limited effectiveness of other control measures. Genomic analysis of biological control agents provides information on the genetic potential of these organisms to control plant disease and useful taxonomic information. In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens, was obtained. Comparative analyses of complete genomes of 105 strains of B. velezensis as well as strains of closely related Bacillus spp. was also performed. The genomes of these B. velezensis strains collectively contained twelve groups of genes involved in the production of antimicrobial compounds, some of which are very effective against plant pathogens. Among these, five groups of genes, for bacilysin, bacillibactin, fengycin, bacillaene and surfactin biosynthesis were present in all genomes, whereas genes for difficidin and macrolactin biosynthesis were present in all but one strain. A total of 19 strains previously identified as Bacillus amyloliquefaciens were reclassified as B. velezensis. This information will be useful to scientists devising strategies for biological control of diseases.

Technical Abstract: In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single chromosome of 3.95 Mbp in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins, and 27 RNA genes. Analyses based on ANI and dDDH and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as B. amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens and 1 was B. siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, ANI and dDDH, and other information about the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens and B. siamensis, with emphasis on their taxonomical status.