A pangenomic study of Bacillus thuringiensis  

作　　者：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 

机构地区：[1]James D. Watson Institute of Genome Sciences, College of Life Science, Zhejiang University, Hangzhou 310058, China [2]CAS Key Laboratory of Genome Science and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China [3]Graduate University of Chinese Academy of Sciences, Beijing 100049, China [4]State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China [5]The Date Palm Genome Project （DPGP）, King Abdulaziz City for Science and Technology （KACST）, P.O. Box： 6086, Riyadh 11442, Kingdom of Saudi Arabia

出　　处：《Journal of Genetics and Genomics》2011年第12期567-576,共10页遗传学报（英文版）

基　　金：supported by a grant from King Abdulaziz City for Science and Technology,Riyadh,Saudi Arabia(No. KACST 428-29);institutional grant from CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics, Chinese Academy of Sciences;supported by the grants from the National Basic Research Program(973 Program)(No.2010CB126604);the Special Foundation Work Program(No.2009FY 120100);the Ministry of Science and Technology of the People's Republic of China and from the National Science Foundation of China(No. 31071163).

摘　　要：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 2.3-2.8 Mb and 5.0-5.6 Mb.We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed,are very useful for pangenomic studies.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 2.3-2.8 Mb and 5.0-5.6 Mb.We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed,are very useful for pangenomic studies.

关 键 词：Bacillus thuringiensis（B.thuringiensis） Pseudo-chromosome Pangenome 

分 类 号：Q987[生物学—遗传学] S476.11[生物学—人类学]