Full genome sequencing was performed using the HiScan™SQ system (Illumina, San Diego, CA, USA), generating 10,785,126 individual readings of 150 bp in length. The genomes of B. amyloliquefaciens Bs006 and P. palleroniana PS006 were assembled using ARGO, a reference-guided assembler developed at NCBI, and SPAdes, a de novo assembler [43 (link)]. The draft genome was annotated using the Rapid Annotation using Subsystem Technology (RAST) server and the nr database, whilst antimicrobial resistance genes (ARGs) were identified using the SARG 2.0 database, RAST server, and nr database. Genome drafts were previously announced in Gamez et al. in 2015 and 2016 [37 (link), 38 (link)]. The COGs (Clusters of Orthologous Groups of proteins) categories were identified using the eggNOG-mapper tool (http://eggnog-mapper.embl.de/ ) employing the default options [44 (link)].
To quantify the number of genes/factors occurring in the genomes of the two strains involved in functions that are relevant in plant–microbe interactions, the online tool PIFAR (Plant–bacteria Interaction Factors Resource) was used [45 (link)].
Secondary metabolites biosynthetic clusters were detected with the antiSMASH tool (https://antismash.secondarymetabolites.org ), using the default setting, and “strict” detection strengthness [46 (link)].
To quantify the number of genes/factors occurring in the genomes of the two strains involved in functions that are relevant in plant–microbe interactions, the online tool PIFAR (Plant–bacteria Interaction Factors Resource) was used [45 (link)].
Secondary metabolites biosynthetic clusters were detected with the antiSMASH tool (
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