Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.
Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.
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DOI：
10.1371/journal.ppat.1003503
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发表时间：
2013
期刊：
影响因子：
6.7
通讯作者：
Templeton MD
中科院分区：
文献类型：
--
作者：
McCann HC;Rikkerink EH;Bertels F;Fiers M;Lu A;Rees-George J;Andersen MT;Gleave AP;Haubold B;Wohlers MW;Guttman DS;Wang PW;Straub C;Vanneste JL;Rainey PB;Templeton MD
作物病害的起源与植物的驯化有关。大多数作物在几个世纪甚至几千年前就被驯化了，因此限制了了解伴随疾病出现的机会。猕猴桃（猕猴桃属）是一个例外：驯化始于20世纪30年代，当时由丁香酸枝引起的溃疡病爆发。actinidiae （Psa）首次记录于20世纪80年代。基于对两个循环基因组和34个草稿基因组的SNP分析，我们发现Psa由不同的进化支组成，进化支内的多样性可以忽略不计，这与来自源群体的独立采样引起的疾病一致。三个分支对应于它们的地理隔离来源；第四种病毒包括导致2008年疫情的Psa-V病毒株，目前已在全球分布。Psa具有整体的克隆群体结构，然而，基因组携带病株内重组的显著特征。Psa-V的SNP分析揭示了数百个多态性；然而，大多数存在于pphgi -1样共轭元件中，其进化与核心基因组无关。由于重组而去除的snp产生了一个无信息的（星形）系统发育，与过去十年单个克隆的Psa-V多样化一致。生长试验证明了Psa-V在猕猴桃中的快速全身运动。基因组比较显示动态基因组与正向选择的证据III型效应和其他候选毒力基因。每个分支都有高度不同的辅助基因编码效应器和毒素，有证据表明通过多种遗传途径获得和失去。血管病原体同源基因仅在Psa-V中发现。我们的分析捕获了一种病原体，在出现的早期阶段，来自与野生猕猴桃物种相关的预测源种群。除了候选基因作为抗性育种计划的目标外，我们的发现还强调了源种群作为新疾病储存库的重要性。尽管上个世纪在植物保护方面取得了相当大的科学进步，但农作物仍然容易受到病原体的感染。集约化栽培，特别是无性繁殖作物的集约化栽培，增加了新疾病出现和迅速传播的可能性。丁香假单胞菌。猕猴桃菌是上世纪80年代中期首次报道的猕猴桃溃疡病致病菌。然而，2008年发生了一次新的疾病暴发，该毒株已在世界各种植区迅速蔓延。为了确定该病原体的起源、种群结构和特征，建立了一个大规模的测序项目。这澄清了不同Psa分离株之间的系统发育关系，并确定了与毒性菌株表现出的侵袭性全身感染策略相关的爆发特异性基因集。这一信息对于制定针对这一严重疾病的强有力的长期解决方案具有不可估量的价值。鉴于商业规模的猕猴桃生产是一个相对较新的事件，该分析为这种病原体与其宿主从首次出现到最近的全球爆发的演变提供了独特的见解。这一认识应有助于减轻未来毁灭性疫情的爆发。
The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease. Despite considerable scientific advances in plant protection during the last century, agricultural crops remain vulnerable to infection by pathogens. The intensive cultivation particularly of clonally propagated crop plants increases the potential for the emergence and rapid spread of new diseases. Pseudomonas syringae pv. actinidiae was first reported as a canker-causing pathogen of kiwifruit in the mid-1980s. However, a new outbreak of the disease occurred in 2008 and this strain has spread rapidly throughout growing regions of the world. In order to determine the origin, population structure and defining features of this pathogen, a large-scale sequencing project was established. This clarified the phylogenetic relationships between the different Psa isolates and identified the outbreak-specific gene sets associated with the aggressive systemic infection strategy exhibited by the virulent strain. This information is invaluable in developing robust long-term solutions for this serious disease. Given that kiwifruit production on a commercial scale is a relatively recent event, this analysis provides a unique insight into the evolution of this pathogen with its host, from its first emergence to the latest global outbreak. This understanding should aid in the mitigation of devastating outbreaks in the future.
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影响因子：
6.7
作者：
Baltrus DA;Nishimura MT;Romanchuk A;Chang JH;Mukhtar MS;Cherkis K;Roach J;Grant SR;Jones CD;Dangl JL
通讯作者：
Dangl JL
DOI：
10.1073/pnas.1731982100
发表时间：
2003-09-02
影响因子：
11.1
作者：
Buell, CR;Joardar, V;Collmer, A
通讯作者：
Collmer, A
DOI：
10.1126/science.1171647
发表时间：
2009-05-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Boller T;He SY
通讯作者：
He SY
影响因子：
6.7
作者：
Arnold R;Brandmaier S;Kleine F;Tischler P;Heinz E;Behrens S;Niinikoski A;Mewes HW;Horn M;Rattei T
通讯作者：
Rattei T
影响因子：
4.2
作者：
Bendtsen JD;Kiemer L;Fausbøll A;Brunak S
通讯作者：
Brunak S