McDonald Megan C, McGinness Lachlan, Hane James K, Williams Angela H, Milgate Andrew, Solomon Peter S
Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 2601.
Black Box Bioinformatics, Perth, WA, Australia 6102 CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia Curtin Institute for Computation, Curtin University, Perth, WA, Australia 6102.
G3 (Bethesda). 2016 Apr 7;6(4):779-91. doi: 10.1534/g3.115.025197.
Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
小麦黄斑叶枯病菌是一种专性寄生于小麦的坏死营养型病原菌。小麦黄斑叶枯病菌的感染特征是其潜伏期较长，通常持续2周，随后是大量寄主细胞死亡以及真菌生物量的快速增殖。这项研究对13个分离株的基因组变异水平进行了表征，我们测定了这些分离株对11个具有不同抗性基因的小麦品种的毒力。在参考分离株IPO323和13个澳大利亚分离株之间，我们鉴定出超过80万个单核苷酸多态性，其中约10%对基因组的编码区域有影响。此外，我们通过从头组装在澳大利亚分离株的基因中鉴定出超过1700个可能的存在/缺失多态性。最后，我们开发了一种基因树分类方法，该方法可以在单个基因比对中快速识别出分离株群体，其序列单倍型与单个小麦品种上的毒力得分相对应。使用这种方法，我们已经鉴定出不到100个候选效应子基因，其基因序列与对携带主要抗性基因的小麦品种的毒力相关。
