Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides.
Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides.
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DOI：
10.1186/s12864-021-07700-4
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发表时间：
2021-06-04
期刊：
影响因子：
4.4
通讯作者：
Barraclough TG
中科院分区：
文献类型：
--
作者：
Peck LD;Nowell RW;Flood J;Ryan MJ;Barraclough TG
近 50% 的作物产量因病虫害而损失，植物和病原体陷入了疾病爆发的放大共同进化过程。由木枯镰刀菌 (Fusarium xylarioides) 引起的咖啡枯萎病在 20 世纪 20 年代首次爆发后，导致西非和中非的咖啡产量大幅下降。成功管理后，该病后来重新出现，到 2000 年代，埃塞俄比亚的阿拉比卡咖啡和东非和中非的罗布斯塔咖啡出现了两次不同的流行病。在这里，我们使用跨越 52 年的六种历史培养物保藏菌株的基因组测序来确定这些反复爆发背后的进化过程。使用 13,782 个单拷贝直向同源物进行的系统基因组重建表明，罗布斯塔种群起源于最初的爆发，而阿拉比卡种群是与其他菌株不同的姐妹进化枝。对参与发病机制的推定效应基因的筛选表明，种群在基因内容和序列上的差异主要是通过谱系内的垂直过程而产生的。然而，15 个假定的效应基因显示出水平获得的证据，与来自尖孢镰刀菌的基因具有密切的同源性。大多数在较宽的支架内占据较小的同源区域，而四个基因的簇占据20Kb的支架，与尖孢镰刀菌移动致病性染色体上包含已知效应基因的区域具有很强的同源性。尽管缺乏与整个移动染色体的匹配，但我们仍然发现与 DNA 转座子密切相关，尤其是先前提出的微型黑斑羚类型，以促进尖孢镰刀菌致病性基因的水平转移。这些发现支持了一个可行的假设，即阿拉比卡咖啡和罗布斯塔咖啡群体通过转座介导的水平转移从尖孢镰刀菌部分获得了不同的效应基因，尖孢镰刀菌共享咖啡作为宿主，并生活在与咖啡间作的其他植物上。我们的结果表明历史基因组学如何帮助揭示使真菌病原体能够与我们抵抗它们的努力保持同步的机制。我们的推定效应基因列表确定了未来可能的真菌控制目标。反过来，对水平转移机制和假定的供体类群的了解可能有助于设计未来的间作策略，最大限度地减少密切相关的镰刀菌类群之间效应基因转移的风险。在线版本包含可在 (10.1186/s12864-021-07700-4) 获取的补充材料。
Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 1920s. After successful management, it later re-emerged and by the 2000s comprised two separate epidemics on arabica coffee in Ethiopia and robusta coffee in east and central Africa. Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks. Phylogenomic reconstruction using 13,782 single copy orthologs shows that the robusta population arose from the initial outbreak, whilst the arabica population is a divergent sister clade to the other strains. A screen for putative effector genes involved in pathogenesis shows that the populations have diverged in gene content and sequence mainly by vertical processes within lineages. However, 15 putative effector genes show evidence of horizontal acquisition, with close homology to genes from F. oxysporum. Most occupy small regions of homology within wider scaffolds, whereas a cluster of four genes occupy a 20Kb scaffold with strong homology to a region on a mobile pathogenicity chromosome in F. oxysporum that houses known effector genes. Lacking a match to the whole mobile chromosome, we nonetheless found close associations with DNA transposons, especially the miniature impala type previously proposed to facilitate horizontal transfer of pathogenicity genes in F. oxysporum. These findings support a working hypothesis that the arabica and robusta populations partly acquired distinct effector genes via transposition-mediated horizontal transfer from F. oxysporum, which shares coffee as a host and lives on other plants intercropped with coffee. Our results show how historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with our efforts to resist them. Our list of putative effector genes identifies possible future targets for fungal control. In turn, knowledge of horizontal transfer mechanisms and putative donor taxa might help to design future intercropping strategies that minimize the risk of transfer of effector genes between closely-related Fusarium taxa. The online version contains supplementary material available at (10.1186/s12864-021-07700-4).
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