Fig. 3

Complete genome sequencing and gene prediction of Bacillus sp. GFP-2. The complete genome was obtained by using Pacbio RSII platform (Pacific Biosciences, CA, USA). After filter and quality control, all clean reads were assembled using the PacBio HGAP Analysis 2.0 and one circular chromosome with 0 gap was constructed for further analysis. The genome of Bacillus sp. GFP-2 was shown as a circular map: from the outer circle inward, each circle displays information about the genome of forward COG-assigned CDS, reverse COG-assigned CDS, forward CDS, reverse CDS, G + C ratio and GC Skew (a). Gene prediction was performed using Glimmer v. 3.02, and functions of the gene products were annotated by BLAST + using NCBI-nr protein database. The rRNA and tRNA genes were identified by using RNAmmer, tRNAscan-SE and Rfam database. Classification of predicted genes and pathways were analyzed by using COGs (b) and KEGG (c) databases. In addition, the RAST online service (http://rast.nmpdr.org/) was used for verification of gene prediction, annotation and classification. The genome circle was draw by CGView application. The antimicrobial peptides were predicted by BLAST+ using the antimicrobial peptide database (APD3). The gene cluster for secondary metabolites (d) and bacteriocins (e) were predicted with online servers antiSMASH 3.0 (https://antismash.secondarymetabolites.org/) and BAGEL3 (http://bagel.molgenrug.nl/) (d)