Bertazzoni Stefania, Jones Darcy A B, Phan Huyen T, Tan Kar-Chun, Hane James K
Centre for Crop & Disease Management, Curtin University, Perth, Australia.
Curtin Institute for Computation, Curtin University, Perth, Australia.
BMC Genomics. 2021 May 25;22(1):382. doi: 10.1186/s12864-021-07699-8.
The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised - ToxA, Tox1 and Tox3.
A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions.
We present an updated series of genomic resources for P. nodorum Sn15 - an important reference isolate and model necrotroph - with a comprehensive survey of its predicted pathogenicity content.
小麦壳针孢菌可引发小麦的颖枯病，是坏死营养型植物病原体的模式物种。参考菌株Sn15的基因组组装于2007年首次报道。小麦壳针孢菌通过产生蛋白质类坏死营养型效应子促进感染，其中三种效应子已得到表征，即ToxA、Tox1和Tox3。
对澳大利亚小麦壳针孢菌参考菌株Sn15进行了染色体水平的基因组组装，该组装结合了长读长测序、光学图谱绘制和人工编辑，得到了23条染色体，其中21条染色体两端均有端粒。新的转录组数据与真菌特异性基因预测技术及人工编辑相结合，生成了一个高质量的预测基因注释数据集，其中包括l3869个高可信度基因，另外还保留了2534个低可信度基因以辅助致病性效应子的发现。与一组来自31个国际来源的菌株进行比较，在Sn15基因组中确定了多个突变或存在-缺失变异的热点区域，用于增强后续效应子预测。效应子预测产生了257个候选效应子，从中选择了98个排名较高的候选效应子进行深入分析，揭示了大量与致病性相关的功能。此外，98个候选效应子中有11个还表现出直系同源保守模式，表明与其他谷物致病真菌物种存在横向基因转移。泛基因组分析表明，长度为0.4 Mbp的最小染色体是一条附属染色体（AC23）。无毒菌株中明显没有AC23，且该染色体以突变热点为主，与其他染色体相比，非同义突变增加。令人惊讶的是，AC23缺乏效应子候选基因，但包含几个具有冗余致病性相关功能的预测基因。
我们提供了一系列更新的小麦壳针孢菌Sn15基因组资源，Sn15是一个重要的参考菌株和坏死营养型模式菌株，并对其预测的致病性内容进行了全面调查。
