The fully resolved genome ofBacillus thuringiensisHER1410 reveals acry-containing chromosome, two megaplasmids & an integrative plasmidial prophage

AbstractBacillus thuringiensisis the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600B. thuringiensisgenomes have been reported, but less than 5% have been resolved, while the other draft genomes are incomplete, precluding plasmid delineation. Here we present the complete genome ofBacillus thuringiensisHER1410, a strain closely related toB. thuringiensis entomocidusand a known host for a variety ofBacillusphages. The combination of short and long-reads techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a uniquecrygene,cry1Ba4,located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368kb), a likely conjugative plasmid involved in virulence, and pLUSID2 potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome, causes the disruption of a flagellar key component. Finally, phylogenetic analysis located this strain within a clade comprising members from theB. thuringiensisserovarthuringiensisand other serovars and withB.cereus s. s.This highlights the intermingled taxonomy ofB. cereus sensu latogroup, where genomics alone does not support the present taxonomy betweenB. cereus s. s.andB. thuringiensisas species designation currently relies solely on the presence of entomocidal genes.ImportanceBacillus cereusgroup species have been extensively studied due to their economical and clinical relevance. This importance originally set the basis forB. cereusgroup members classification which are commonly based on phenotypical criteria. Sequencing era has shed light about genomic characterization of these species, showing their chromosomal genomic similarity and highlighting the role of mobile genetic elements, especially megaplasmids, in the classification and characterization of this group. However, only the 5% of the sequencedB. thuringiensisgenomes have been fully resolved. Thus, here we addressed efficiently the studyB. thuringiensisHER1410 genomic features by the use of a combination of short and long-reads sequencing. This methodology resulted in the high-quality assembly, which led to the identification of an uncommon location of acrygene close to the chromosomal origin, as well as three fully resolved extrachromosomal elements, two megaplasmids and an integrative plasmidial prophage.