Abstract：
Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their \"core biology\", being present, functional and expressed by all strains or \"flexible biology\", varying between strains. Genes supporting flexible biology may be considered to be \"accessory\", whilst the \"core\" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study.
We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a \"core\" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression.
These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a \"core\" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression.
These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
摘要：
背景：研究快速进化的病原体中的基因组变异可能有助于鉴定支持其“核心生物学”的基因，在场,功能和由所有菌株或“灵活生物学”表达，在菌株之间变化。支持柔性生物学的基因可以被认为是“附件”，虽然“核心”基因集可能对病原体物种生物学的共同特征很重要，包括对所有宿主基因型的毒力。小麦致病性真菌Trymoseptoria代表了对全球粮食安全发展最快的威胁之一，是本研究的重点。
结果：我们构建了18个欧洲田间分离株的pangenome，12在感染期间也进行了RNAseq转录谱分析。结合这些数据，我们预测了一个包含9807个序列的“核心”基因集，这些序列(1)存在于所有分离株中，（2）缺乏失活多态性和（3）所有分离株表达。一个大的附属基因组，由总基因的45%组成，也被定义了。我们在染色体和个体基因尺度上对遗传和基因组多态性进行了分类。包括毒力在内的基本功能所需的蛋白质在核心基因之间具有低于平均的序列变异性。核心和附属基因组都编码了许多小的，分泌的可能与植物免疫相互作用的候选效应蛋白。病毒载体介导的短暂在植物中过表达88个候选物，未能鉴定出任何引起叶片坏死的疾病特征。然而,缺乏五个核心基因的非致病性缺失突变体的功能互补表明，通过重新引入表现出最小序列多态性和最高表达的单个基因，可以恢复完全的毒力。
结论：这些数据支持pangenomics和转录组学的联合使用来定义代表核心基因，并且可能被利用，在快速进化的病原体的弱点。
结果：我们构建了18个欧洲田间分离株的pangenome，12在感染期间也进行了RNAseq转录谱分析。结合这些数据，我们预测了一个包含9807个序列的“核心”基因集，这些序列(1)存在于所有分离株中，（2）缺乏失活多态性和（3）所有分离株表达。一个大的附属基因组，由总基因的45%组成，也被定义了。我们在染色体和个体基因尺度上对遗传和基因组多态性进行了分类。包括毒力在内的基本功能所需的蛋白质在核心基因之间具有低于平均的序列变异性。核心和附属基因组都编码了许多小的，分泌的可能与植物免疫相互作用的候选效应蛋白。病毒载体介导的短暂在植物中过表达88个候选物，未能鉴定出任何引起叶片坏死的疾病特征。然而,缺乏五个核心基因的非致病性缺失突变体的功能互补表明，通过重新引入表现出最小序列多态性和最高表达的单个基因，可以恢复完全的毒力。
结论：这些数据支持pangenomics和转录组学的联合使用来定义代表核心基因，并且可能被利用，在快速进化的病原体的弱点。
