title: A pangenomic study of Bacillus thuringiensis.
abstract: Bacillus thuringiensis (B. thuringiensis) is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins (Cry) are commonly used as biological alternatives to pesticides. In a pangenomic study, we sequenced seven B. thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform. The B. thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added. Compared to the pangenomes of its closely related species of the same genus, B. thuringiensis pangenome shows an open characteristic, similar to B. cereus but not to B. anthracis; the latter has a closed pangenome. We also found extensive divergence among the seven B. thuringiensis genome assemblies, which harbor ample repeats and single nucleotide polymorphisms (SNPs). The identities among orthologous genes are greater than 84.5% and the hotspots for the genome variations were discovered in genomic regions of 2.3-2.8Mb and 5.0-5.6Mb. We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed, are very useful for pangenomic studies.
authors.affiliation: James D. Watson Institute of Genome Sciences, College of Life Science, Zhejiang University, Hangzhou 310058, China.
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Fang
authors.forename: Zhaolong
authors.initials: Z
authors.lastname: Li
authors.forename: Jiucheng
authors.initials: J
authors.lastname: Liu
authors.forename: Changlong
authors.initials: C
authors.lastname: Shu
authors.forename: Xumin
authors.initials: X
authors.lastname: Wang
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhang
authors.forename: Xiaoguang
authors.initials: X
authors.lastname: Yu
authors.forename: Duojun
authors.initials: D
authors.lastname: Zhao
authors.forename: Guiming
authors.initials: G
authors.lastname: Liu
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Al-Mssallem
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001413:Bacillus thuringiensis / Q000145:classification / Q000235:genetics*; D000083722:Bacillus thuringiensis Toxins; D001426:Bacterial Proteins / Q000235:genetics; D004252:DNA Mutational Analysis; D004731:Endotoxins / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D006460:Hemolysin Proteins / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids; D017422:Sequence Analysis, DNA
chemical_list: D000083722:Bacillus thuringiensis Toxins; D001426:Bacterial Proteins; D004731:Endotoxins; D006460:Hemolysin Proteins; C030956:insecticidal crystal protein, Bacillus Thuringiensis