Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Abstract

Background: In this study, the Bacillus sp. strain BH32 (a plant-beneficial bacterial endophyte) and its closest non-type Bacillus cereus group strains were used to study the organization, conservation, and diversity of biosynthetic gene clusters (BGCs) among this group to propose a classification framework of gene cluster families (GCFs) among this intricate group. A dataset consisting of 17 genomes was used in this study. Genomes were annotated using PROKKA ver.1.14.5. The web tool antiSMASH ver. 5.1.2 was used to predict the BGCs profiles of each strain, with a total number of 198 BGCs. The comparison was made quantitatively based on a BGCs counts matrix comprising all the compared genomes and visualized using the Morpheus tool. The constitution, distribution, and evolutionary relationships of the detected BGCs were further analyzed using a manual approach based on a BLASTp analysis (using BRIG ver. 0.95); a phylogenetic analysis of the concatenated BGCs sequences to highlight the evolutionary relationships; and the conservation, distribution and the genomic co-linearity of the studied BGCs using Mauve aligner ver. 2.4.0. Finally, the BIG-SCAPE/CORASON automated pipeline was used as a complementary strategy to investigate the gene cluster families (GCFs) among the B. cereus group. Results: Based on the manual approach, we identified BGCs conserved across the studied strains with very low variation and interesting singletons BGCs. Moreover, we highlighted the presence of two major BGCs synteny blocks (named “synteny block A” and “synteny block B”), each composed of conserved homologous BGCs among the B. cereus group. For the automatic approach, we identified 23 families among the different BGCs classes of the B. cereusgroup, named using a rational basis. The proposed manual and automatic approaches proved to be in harmony and complete each other, for the study of BGCs among the selected genomes. Conclusion: Ultimately, we propose a framework for an expanding classification of the B. cereus group BGCs, based on a set of reference BGCs reported in this work.