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.

Keywords: Bacillus cereus sensu lato; Bacillus thuringiensis; Pan-Core-genome; Parasporal crystal protein; Prophages.

Fig. 1

Microscopic characteristics of 10.1601/nm.5000 MYBT18246. a Light microscope analysis of Gram stained 10.1601/nm.5000 MYBT18246 cells (40×). b Phase contrast microscope analysis of sporulated and Cry-toxin producing cells of 10.1601/nm.5000 MYBT18246 (40×)

Fig. 2

Phylogenetic tree highlighting the taxonomic relation of 10.1601/nm.5000 MYBT18246 (red) based on a) 16rDNA amplicon within the 10.1601/nm.4857 clade b) Multi-locus sequence typing within the 10.1601/nm.4885 sensu lato species group. GenBank accession numbers are given in parentheses. Comparison includes strains of the 10.1601/nm.4854 clade or Bcsl group members (blue). 10.1601/nm.5141 10.1601/strainfinder?urlappend=%3Fid%3DDSM+25430 or 10.1601/nm.4858 str. 168 has been used as outlier to root the tree. Sequences were aligned using ClustalW 1.6 [91, 92]. The phylogenetic tree was constructed by using the Neighbor-Joining method [50] and evolutionary distances were computed by the Maximum Composite Likelihood method [51] within MEGA7.0 [52]. Numbers at the nodes are bootstrap values calculated from 1000 replicates

Fig. 3

Circular visualization of the genome comparison of 10.1601/nm.5000 MYBT18246 with 3 other sequenced 10.1601/nm.5000 strains. The tracks from the outside represent: (track 1–2) Genes encoded by the leading and lagging strand of 10.1601/nm.5000 MYBT18246 marked in COG colors [93]; (track 3) putative prophage regions, identified with PHAST in blue [76], (track 4) identified cry toxin genes in red; (track 5–7) orthologs for the genomes of 10.1601/nm.5000 YBT-1518 (CP005935.1), 10.1601/nm.5000 CT-43 (CP001907.1), 10.1601/nm.5000 Bt407 (CP003889.1) illustrated in red to light yellow, singletons in grey (grey: <1e⁻²⁰; light yellow: 1e⁻²¹–1e⁻⁵⁰; gold: 1e⁻⁵¹–1e⁻⁹⁰; light orange: 1e⁻⁹¹–1e⁻¹⁰⁰; orange: 1e⁻¹⁰¹–1e⁻¹²⁰; red: >1e⁻¹²¹ (track 7) % GC plot (track 8), GC skew [(GC)/(G + C)]. Visualization was done with DNAPlotter [94]

Fig. 4

Venn diagram of the genome comparison of 10.1601/nm.5000 MYBT18246 with other 10.1601/nm.5000 strains. Venn diagram displays the orthologous genes between 10.1601/nm.5000 MYBT18246 (CP015350-CP015361), 10.1601/nm.5000 YBT-1518 (CP005935-CP002486), 10.1601/nm.5000 serovar chinensis CT-43 (CP001907-CP001917) and 10.1601/nm.5000 Bt407 (CP003889-CP003898). Ortholog detection was performed with Proteinortho [84] including protein blast with a similarity cut-off of (50%) and an E-value of 1e⁻¹⁰. The total number of genes and paralogs are depicted under the corresponding species name. Open reading frames that were classified as pseudogenes were not included in this analysis