Integrative Analysis of Genome, Transcriptome and Epigenome Data from Coevolved Bacillus Thuringiensis Strains CLUSTER: "Experimental Evolution and Natural Variation of Bacillus-Invertebrate Interactions"

在拟议的项目中，将调查寄生虫和宿主在进化过程中的相互基因组适应及其对基因活性的影响。因此，基因组、转录组和表观基因组数据将通过高通量测序方法产生。首先，将对苏云金芽孢杆菌MBYT18247和407在三个宿主-寄生虫协同进化实验中的突变事件进行量化、表征和定位。这些数据将通过a)高覆盖率基因组测序来确定序列变异，以及b)单分子测序来确定原始材料和进化材料中宿主和寄生虫基因组的甲基化状态。为了确定与菌株适应相关的突变，将对进化实验中不同时间点的寄生虫/宿主样本进行基于RNA-seq的比较转录分析。这样产生的数据将用生物信息学方法进行“深入”分析，并用于开发寄生虫基因组的动态结构模型。在野生型菌株上对突变基因进行靶点重组，然后进行感染实验，可以对不同活性和表型的突变基因进行功能分析。功能分析是最终的实验工作。建议的实验有望深入了解苏云金芽孢杆菌的进化机制，由于基因组结构的高度相似性，可能会推广到整个芽孢杆菌属。

In the proposed project the reciprocal genomic adaptations of parasites and hosts during evolutionary processes and their impact on the gene activity shall be investigated. Therefore genome-, transcriptome- and epigenome data will be produced by high throughput sequencing methods. First a quantification, characterization and localization of the mutation events during three host-parasite coevolution experiments with Bacillus thuringiensis MBYT18247 and 407 will be performed. The data will be generated by a) high coverage genome sequencing for the determination of sequence variation and b) single molecule sequencing for the determination of the methylation status of host and parasite genomes from the original and the evolved material. To identify mutations relevant for strain adaptation a comparative RNA-seq based transcription analysis of parasite/host samples from different time points of the evolution experiment will be performed. The thus generated data shall be analyzed in an “in depth” analysis with bioinformatics methods and be used to develop a dynamic structural model of the parasite genome. A functional analysis of mutated genes with varied activity and phenotype might be done by the target reconstruction of the mutants on wild type strains followed by infection experiments. The functional analysis represents the final experimental work. The suggested experiments promise insights in the evolutionary mechanisms of the species Bacillus thuringiensis which might, due to the high similarity of genome structures, may be generalized to the whole genus Bacillus.