A pangenomic study of Bacillus thuringiensis

Yongjun Fang; Zhaolong Li; Jiucheng Liu; Changlong Shu; Xumin Wang; Xiaowei Zhang; Xiaoguang Yu; Duojun Zhao; Guiming Liu; Songnian Hu; Jie Zhang; Ibrahim Al-Mssallem; Jun Yu

doi:10.1016/j.jgg.2011.11.001

Volume 38 Issue 12

Dec. 2011

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A pangenomic study of Bacillus thuringiensis

doi: 10.1016/j.jgg.2011.11.001

Yongjun Fang^{a, e, #},
Zhaolong Li^{b, c, #},
Jiucheng Liu^{b, e, #},
Changlong Shu^d,
Xumin Wang^b,
Xiaowei Zhang^{b, e},
Xiaoguang Yu^{b, e},
Duojun Zhao^{b, e},
Guiming Liu^{b, e},
Songnian Hu^{b, e},
Jie Zhang^d,
Ibrahim Al-Mssallem^e,
Jun Yu^{a, b, c, e}

a
James D. Watson Institute of Genome Sciences, College of Life Science, Zhejiang University, Hangzhou 310058, China
b
CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
c
Graduate University of Chinese Academy of Sciences, Beijing 100049, China
d
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
e
The Date Palm Genome Project (DPGP), King Abdulaziz City for Science and Technology (KACST), P.O. Box: 6086, Riyadh 11442, Kingdom of Saudi Arabia

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Corresponding author: E-mail address: jzhang@ippcaas.cn (Jie Zhang); E-mail address: imssallem@kacst.edu.sa (Ibrahim Al-Mssallem); E-mail address: junyu@big.ac.cn (Jun Yu)
Received Date: 2011-07-24
Accepted Date: 2011-11-09
Rev Recd Date: 2011-10-25

Available Online: 2011-11-15

Publish Date: 2011-12-20

Abstract

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.
- Pseudo-chromosome,
- Pangenome

These authors contributed equally to this work.

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References(48)

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