James D. Watson Institute of Genome Sciences, College of Life Science, Zhejiang University, Hangzhou 310058, China.
J Genet Genomics. 2011 Dec 20;38(12):567-76. doi: 10.1016/j.jgg.2011.11.001. Epub 2011 Nov 15.
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.
苏云金芽孢杆菌（B. thuringiensis）是一种土壤居住的革兰氏阳性细菌，其质粒编码的毒素（Cry）通常被用作农药的生物替代品。在全基因组研究中，我们使用下一代测序平台对 7 个苏云金芽孢杆菌分离株进行了高覆盖率和碱基质量测序。当添加一个新的基因组时，苏云金芽孢杆菌的泛基因组被推断具有 4196 个核心基因和一个渐近值为 558 个独特基因。与同一属的密切相关的物种的泛基因组相比，苏云金芽孢杆菌的泛基因组表现出开放的特征，类似于蜡状芽孢杆菌，但不同于炭疽芽孢杆菌；后者具有封闭的泛基因组。我们还发现了 7 个苏云金芽孢杆菌基因组组装之间的广泛分歧，这些分歧中存在大量的重复序列和单核苷酸多态性（SNP）。直系同源基因之间的同一性大于 84.5%，基因组变异的热点位于 2.3-2.8Mb 和 5.0-5.6Mb 的基因组区域。我们得出结论，在所有缺口都闭合之前，来自多个菌株的高覆盖率序列组装对于泛基因组研究非常有用。
