Data on genome analysis of Bacillus velezensis LS69

The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.


Data source location
Bacillus velezensis LS69 was isolated from the rice field of Lichuan city, Hubei Province (China).

Data accessibility
The whole genome sequence of B. velezensis LS69 has been deposited in GenBank under the accession number CP015911.

Value of the data
Bacillus velezensis LS69 were found to contain an abundant of gene clusters required for synthesizing antimicrobial metabolites and promoting plant growth. Most of unique genes for strain LS69 were clustered in the seven genetic islands. Here we provided an detailed analysis of the genes on the genetic islands.
Bacillus velezensis strains were known to produce versatile metabolites with antimicrobial activity and secrete a variety of compounds promoting plant-growth. Here we provided an analysis of the COG distribution of the core genes, accessory genes and the unique genes in 12 B. velezensis strains.
Our data provide an extended analysis of the amylolysin cluster, which was found to be unique for the B. velezensis LS69 by comparative analysis with the highly homologous B. velezensis strains.

Data
Genomic islands are clusters of genes of probable horizontal origin, and they usually play an important role in antimicrobial resistance and virulence in microbes [2]. Fig. 1 shows the seven genomic islands predicted in the Bacillus velezensis LS69. Supplementary Table 1 provides an overview of the genes on the genetic islands. In the B. velezensis LS69, most of the unique genes were clustered on these islands. Fig. 2 shows the COG distribution of the core genes, accessory genes and the unique genes in 12 B. velezensis strains. Fig. 3 provides an extended analysis of the amylolysin cluster in B. velezensis LS69 and the corresponding genetic loci in other B. velezensis strains.

Prediction of the NRPS, PKS and bacteriocins gene clusters involved in synthesis of secondary metabolites
Bioinformatic tools antiSMASH [4] and BAGEL3 [5] were used to mining for the gene clusters involved in synthesizing polyketides and bacteriocins. 34 potential gene clusters were predicted in the strain LS69. Through comparative analysis with the clusters reported, ten gene clusters were found to be involved in nonribosomal synthesis of polyketides and bacteriocins. The reference gene clusters were download from the NCBI (these reference sequences are supported by corresponding papers). The accession number of the reference sequences for annotation and comparison were shown: surfactin of Bacillus subtilis (locus_tag of the srfABCD,ycxA,sfp,yczE: BSU03480/BSU03490/ BSU03510/BSU03520/BSU03530/BSU03570/BSU03580); iturin of Bacillus subtilis (GenBank: AB050629.1); fengycin of Bacillus subtilis (GenBank accession number of the fenABCDE: AF023464/

Extended analysis of the amylolysin cluster in B. velezensis LS69
The amylolysin cluster was predicted by using BAGEL3, and annotated by comparative analysis with the corresponding cluster reported in B. amyloliquefaciens GA1 (whole genome sequence of strain GA1 has not yet been made public). Extended analysis showed the 16 kb fragment (including the amylolysin cluster) was unique for the strain LS69. This fragment was missing in the other highly homologous B. velezensis strains (FZB42, YJ11-1-4, CAU B946, JJ-D34, JS25R, NAU-B3, UCMB5033, UCMB5113 and YAU B9601-Y2).  velezensis strains, one 16 kb fragment was found to be unique for the strain LS69. This genetic loci was predicted to be mainly involved in synthesizing amylosin in B. velezensis LS69 by blast analysis (Green box shows the core cluster of amylosin by comparative with the amylosin reported in B. amyloliquefaciens GA1. In B. velezensis FZB42 and other B. velezensis strains, the corresponding loci was found to encode anion permease. The flanking sequences of amylolysin loci share over 98% sequence identity in strain LS69 and other B. velezensis strains. The flanking sequences encode the same proteins altronate hydrolase and hypothetical protein.