Comprehensive Annotation of the <i>Parastagonospora nodorum</i> Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.颖枯壳针孢（Parastagonospora nodorum）是引发颖枯病（Septoria nodorum blotch, SNB）的病原菌，亦是小麦（Triticum spp.）的重要经济病原真菌，同时也是研究死体营养型病理学与基因组进化的模式生物。参考菌株P. nodorum SN15是首个发布基因组序列的座囊菌纲（Dothideomycete）真菌，已被广泛应用于物种种内及种间的比较研究。本研究报道了一套更新版的参考基因组组装结果：基于深度重测序数据修正了原始基因组组装中的单核苷酸多态性（SNP）与插入缺失（indel）错误，并结合转录组学与蛋白质组学证据对基因模型开展了详尽的人工注释（https://github.com/robsyme/Parastagonospora_nodorum_SN15）。更新后的组装与注释集合包含8366个经过蛋白序列修正的基因，以及866个全新基因。本研究证实，结合多种实验方法与专家人工注释，可获得一套可靠的基因模型集。