Pan-genome and phylogeny of Bacillus cereus sensu lato.
Pan-genome and phylogeny of Bacillus cereus sensu lato.
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DOI：
10.1186/s12862-017-1020-1
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发表时间：
2017-08-02
影响因子：
3.4
通讯作者：
Bazinet AL
中科院分区：
文献类型：
--
作者：
Bazinet AL
广义蜡状芽孢杆菌（Bacillus cereus lato）（l.）是一个具有医学和农业意义的生态多样性细菌群。在这项研究中，我使用公开的基因组和新的生物信息学工作流程来表征B。塞雷乌斯湾L.泛基因组，并执行最大的系统发育和人口遗传分析，这一组迄今为止的基因和类群的数量。有了这些基本数据，我确定了与特定表型性状相关的基因（即，“泛GWAS”分析），并量化共享共同属性的分类群在遗传学上聚类的程度。使用基于快速k-mer的方法（Mash）来创建所选芽孢杆菌基因组的简化表示，并对该数据进行基于距离的快速系统发育分析（FastME），以确定哪些物种应包括在B中。塞雷乌斯湾L.八个B的完整基因组。塞雷乌斯湾L.物种用Prokka重新注释，Roary使用这些注释产生B。塞雷乌斯湾L.泛基因组Scoary用于将基因存在和缺失模式与各种表型相关联。过滤Roary产生的正向同源蛋白质序列簇，并用于构建基因模型的HaMStR数据库，这些基因模型又用于构建系统发育数据矩阵。系统发育分析使用RAxML、DendroPy、ClonalFrameML、PAUP* 和SplitsTree。基于贝叶斯模型的群体遗传分析使用hierBAPS将分类群分配到聚类。系统分类指数被用来量化具有共同属性的分类群的系统聚类。B。塞雷乌斯湾L.泛基因组目前由160，000个基因组成，其中1600个是“核心”基因（至少99%的样本分类群共有）。Pan-GWAS分析揭示了与表型相关的基因，如隔离源，氧气需求，以及导致炭疽或食物中毒等疾病的能力。广泛的系统发育分析，使用前所未有的大量数据产生的同源性，在很大程度上是一致的，彼此和与以前的研究。系统发育支持率的自举概率显着增加时，所有合适的泛基因组数据包括在系统发育分析，而不是只使用核心基因。贝叶斯群体遗传分析建议将B分为三个主要分支。塞雷乌斯湾L.分为九个集群。具有共同特征和物种名称的类群表现出不同程度的系统发育聚类。所有的系统发育分析概括了两个以前使用的分类系统，并始终被分配到相同的主要分支和组的类群。通过在系统发育分析中包括来自泛基因组的辅助基因，我产生了114个完全B的异常支持的系统发育。塞雷乌斯湾L.基因组最好的方法被用来产生所有498个公开的B的同源性。塞雷乌斯湾L.基因组，这反过来又被用来比较三个不同的分类系统，并测试单系状态的各种B。塞雷乌斯湾L.物种本研究中使用的大多数方法是通用的，可以用来产生泛基因组估计和其他细菌群体的类似的强大的系统发育假设。本文的在线版本（doi：10.1186/s12862-017-1020-1）包含补充材料，可供授权用户使用。
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 and novel bioinformatic workflows 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. 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 produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes. The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are “core” (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering. All phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups. The online version of this article (doi:10.1186/s12862-017-1020-1) contains supplementary material, which is available to authorized users.
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影响因子：
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