Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.
Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.
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DOI：
10.3389/fmicb.2015.00996
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发表时间：
2015
影响因子：
5.2
通讯作者：
Kliebenstein DJ
中科院分区：
文献类型：
--
作者：
Atwell S;Corwin JA;Soltis NE;Subedy A;Denby KJ;Kliebenstein DJ
病原体内部的长期遗传变异如何有助于宿主/病原体相互作用的多样性尚不清楚，部分原因是大多数研究的病原体是宿主特有的克隆繁殖生物，这使得遗传分析变得复杂。相比之下，灰霉病菌是一种有性繁殖的真正单倍体的子囊菌，可以侵染多种植物宿主。虽然以前的工作已经显示了两个分离物之间的显著基因组变异，但我们继续评估了灰霉病菌种群中的站立变异的水平和频率。为了开始测量B.cinerea的长期遗传变异，我们对13个不同分离物的基因组进行了重新测序，并将它们与之前测序的T4参考基因组进行了比对。此外，从四个独立重复的培养物中对其中一个分离株进行了重新测序。13个菌株具有较高的遗传多样性。在这个变异中，我们可以确定具有主效多态的基因簇，即导致预测的功能敲除的多态，这些多态围绕着参与控制营养不亲和性的基因。在营养融合分析中，这些基因座上的基因型能够部分预测这些菌株之间的相互作用，表明这些基因座控制着营养不亲和性。这表明灰霉病菌内的营养不亲和性基因座与遗传多样性增加的区域相关。对独立繁殖了10多年的一个分离物(葡萄)的四个克隆的基因组重新测序显示，没有检测到自发突变。这表明，灰霉病菌没有表现出较高的自发突变率。未来的工作将使我们能够测试这种多样性是否以及如何有助于病原体的广泛宿主范围。
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.