Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246

Abstract

10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA’s. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis

“…The so-called Feature Frequency Profiles (FFP) method implicating SNPs’ acquisition across the Bacullis genome thoroughly outstripped single loci-emanated phylogenies in terms of precision and efficiency, preserving the monophyletic status of B. thuringiensis , B. anthracis , and B. cereus [ 71 ]. Yet another recent study utilized SNP-based phylogeny to dissect close evolutionary interconnection in Bti strains [ 15 ]. Aside from Bt , the application of SNPs for phylogeny reconstruction exhibited fine genomic clarification in other bacterial species, including Escherichia [ 72 ], Burkholderia [ 73 ], and Bacillus cytotoxicus [ 74 ].…”

“…Roary was launched with a 95% identity cutoff for blastp in alignment mode, allowing to retrieve core genes’ alignments. We also increased the maximum number of clusters to 100,000 as Bacillus species are characterized by the acquisition of non-essential genes resulting in genomic variability [ 15 ]. Forasmuch as way too many genes in a pangenome may indicate the inappropriate quality of the underlying data and diminish the analysis’s predictive accuracy [ 104 ], we proposed a simple metric somewhat by analogy with N50.…”

“…Although most of these determinants are detectable at the genomic level, proteomic assays may provide essential evidence for their distribution. To date, both genomic and proteomic techniques are utilized in Bt studies, although the number of comparative proteomics papers [ 10 , 11 ] is considerably smaller than that of works on comparative genomics [ 12 , 13 , 14 , 15 ]. Ideally, the genomic and proteomic approaches should be used in parallel in order to detect virulence factors that are either missing in the proteome screening [ 16 ] or misannotated in the genomic data [ 17 ].…”

Genomic Characterization and Probiotic Potency of Bacillus sp. DU-106, a Highly Effective Producer of L-Lactic Acid Isolated From Fermented Yogurt

“…The gene families were extracted by Hcluster-sg 0.5.1 with default parameters ( Lopes et al, 2017 ). Orthologous genes between all organisms were detected with Proteinortho ( Lechner et al, 2011 ) including protein blast with a similarity cut-off of (50%) and an E -value of 1e −10 ( Hollensteiner et al, 2017 ). Multiple sequence alignment was performed using PRANK v140110 ( Loytynoja and Goldman, 2005 ).…”

Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis

“… 2002 ) and VIP (Hollensteiner et al. 2017a ). In addition, most of the entomotoxin genes are located inside or adjacent to mobile entities (see below) such as insertion sequences (IS), composite and complex transposons (Tn) (Léonard, Chen and Mahillon 1997 ; Rosso, Mahillon and Delécluse 2000 ; Murawska, Fiedoruk and Swiecicka 2014 ).…”