Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia.
Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia.
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DOI：
10.3389/fpls.2017.00148
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发表时间：
2017
影响因子：
5.6
通讯作者：
Park RF
中科院分区：
文献类型：
--
作者：
Wu JQ;Sakthikumar S;Dong C;Zhang P;Cuomo CA;Park RF
叶锈病是小麦最常见的病害之一，由专性生物营养型担子菌--小麦柄锈菌（Pucciniatriticina，Pt）引起。在本研究中，使用全基因组测序分析了来自澳大利亚的20个Pt分离株，其中包括10个表型匹配的对，对Lr 20具有相反的致病性。与美国Pt分离物1-1 BBBD Race 1的参考基因组相比，每个分离物平均发现404，690个单核苷酸多态性（SNP），并且大多数分离物的杂合SNP比例在87%以上，显示出高水平的多态性和高杂合率。从全基因组的SNPs，系统发育树推断，其中包括一个大的分支的15个菌株代表不同的假定克隆谱系，包括14个密切相关的分离物和更分歧的分离物670028，和一个小的分支的5个菌株的特征在于较低的杂合性水平。主成分分析检测到三个不同的集群，完全对应的两个主要子集的小分支和大的分支，包括所有15个分离株，没有进一步分离的分离株670028。虽然全基因组关联分析鉴定出302个基因含有至少一个与Lr 20毒力相关的SNP（p < 0.05），但Wilcoxon秩和检验显示，36个和68个基因在Lr 20无毒力组和毒力组之间的非同义突变计数分别具有显著（p < 0.05）和轻微显著（p < 0.1）差异。预测这些基因中的20个具有不具有跨膜区段的信号肽，并因此鉴定为对应于Lr 20的候选效应基因。SNP分析还暗示了表观遗传学和小RNA在Pt致病性中的潜在参与。因此，未来的研究是必要的，以调查候选效应的生物学功能，以及在表观遗传和转录后水平的基因调控机制。我们的研究是第一个整合表型-基因型关联与Pt基因组中的效应子预测，这种方法可以规避与专性锈菌合作的一些技术困难，并加速无毒基因的鉴定。
Leaf rust is one of the most common and damaging diseases of wheat, and is caused by an obligate biotrophic basidiomycete, Puccinia triticina (Pt). In the present study, 20 Pt isolates from Australia, comprising 10 phenotype-matched pairs with contrasting pathogenicity for Lr20, were analyzed using whole genome sequencing. Compared to the reference genome of the American Pt isolate 1-1 BBBD Race 1, an average of 404,690 single nucleotide polymorphisms (SNPs) per isolate was found and the proportion of heterozygous SNPs was above 87% in the majority of the isolates, demonstrating a high level of polymorphism and a high rate of heterozygosity. From the genome-wide SNPs, a phylogenetic tree was inferred, which consisted of a large clade of 15 isolates representing diverse presumed clonal lineages including 14 closely related isolates and the more diverged isolate 670028, and a small clade of five isolates characterized by lower heterozygosity level. Principle component analysis detected three distinct clusters, corresponding exactly to the two major subsets of the small clade and the large clade comprising all 15 isolates without further separation of isolate 670028. While genome-wide association analysis identified 302 genes harboring at least one SNP associated with Lr20 virulence (p < 0.05), a Wilcoxon rank sum test revealed that 36 and 68 genes had significant (p < 0.05) and marginally significant (p < 0.1) differences in the counts of non-synonymous mutations between Lr20 avirulent and virulent groups, respectively. Twenty of these genes were predicted to have a signal peptide without a transmembrane segment, and hence identified as candidate effector genes corresponding to Lr20. SNP analysis also implicated the potential involvement of epigenetics and small RNA in Pt pathogenicity. Future studies are thus warranted to investigate the biological functions of the candidate effectors as well as the gene regulation mechanisms at epigenetic and post-transcription levels. Our study is the first to integrate phenotype-genotype association with effector prediction in Pt genomes, an approach that may circumvent some of the technical difficulties in working with obligate rust fungi and accelerate avirulence gene identification.