Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.
Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.
BMC Genomics. 2018 Apr 23;19(1):279. doi: 10.1186/s12864-018-4680-3.
Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen.
Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9 Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets.
Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported at the whole genome level, as phylogenetic analysis did not cluster the ToxA producing isolates. This expansion of available Ptr genomics resources will directly facilitate research aimed at controlling tan spot disease.
禾旋孢腔菌（Ptr）是一种坏死型真菌病原体，可引起小麦主要病害——叶枯病。我们旨在提供必要的基于基因组学的资源，以更好地了解这种重要病原体的致病性机制。
在此，我们展示了 8 个新的 Ptr 分离株基因组，经过组装和注释；代表了 1、2 和 5 个小种，以及一个新的小种。我们报告了一个高质量的 Ptr 参考基因组，该基因组由 PacBio 技术测序，Illumina 配对末端数据支持和光学图谱。使用两种酶混合方法，估计基因组覆盖率的 98%映射到 10 个染色体组上。最终的参考基因组为 40.9 Mb，包含总共 13797 个注释基因，转录组和蛋白质基因组数据集提供支持。
全基因组比较分析显示主要的染色体片段重排和融合，突出了该物种的种内基因组可塑性。此外，全基因组水平上不支持 Ptr 小种分类，因为系统发育分析并未将产 ToxA 的分离株聚类在一起。这些 Ptr 基因组学资源的扩展将直接促进控制叶枯病的研究。
