Pan-genome and phylogeny of Bacillus cereus sensu lato

Background: Bacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., \"pan-GWAS\" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered. Methods: A rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produc...背景：蜡样芽孢杆菌广义群（Bacillus cereus sensu lato，以下简称s. l.）是一类生态多样性丰富、兼具医学与农业重要性的细菌类群。本研究利用公开可用的基因组数据，对蜡样芽孢杆菌广义群的泛基因组（pan-genome）进行表征，并开展了迄今为止该类群规模最大的系统发育与群体遗传学分析，涵盖的基因与类群数量均为当前之最。依托这些基础数据，本研究鉴定了与特定表型性状相关的基因（即“泛基因组全基因组关联分析（pan-GWAS）”），并量化了具有共同特征的类群在系统发育上的聚集程度。 方法：本研究采用基于k-mer的快速分析工具Mash对所选芽孢杆菌基因组进行降维表征，随后借助基于距离的快速系统发育分析工具FastME对该数据集开展分析，以确定哪些类群应归入蜡样芽孢杆菌广义群。研究人员对8株蜡样芽孢杆菌广义群物种的完整基因组使用Prokka进行从头注释，并利用Roary基于上述注释结果生成...