Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity.

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 4 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 mating assays showing that these loci control vegetative incompatibility. This suggests that the vegetative mating 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 ten 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.

目前学界对病原体体内的现存遗传变异如何促成宿主-病原体互作的多样性仍知之甚少，部分原因在于绝大多数已研究的病原体均为宿主特异性的无性繁殖生物，这一特性增加了遗传分析的复杂度。与之形成鲜明对比的是，灰葡萄孢（Botrytis cinerea）是一种可进行有性繁殖的真正单倍体子囊菌，能够侵染广泛多样的植物宿主。尽管既往研究已在两株分离株间发现了显著的基因组差异，本研究仍旨在评估灰葡萄孢种群中现存遗传变异的水平与发生频率。为量化灰葡萄孢的现存遗传变异，我们对13株不同的分离株进行了基因组重测序，并将测序结果比对至已发布的T4参考基因组。此外，我们还从4次独立重复培养的培养物中，对其中一株分离株开展了重测序。13株分离株间存在高水平的遗传多样性。在该遗传变异中，我们鉴定到了一批携带主要效应多态性的基因簇——这类多态性可导致预测的功能敲除——且这些基因簇围绕着参与调控营养体不亲和性的基因。这些基因座的基因型可在一定程度上预测分离株在营养体交配实验中的互作模式，表明这些基因座正是调控营养体不亲和性的关键位点。上述结果表明，灰葡萄孢体内的营养体交配基因座与遗传多样性升高的基因组区域存在关联。对一株经十年独立传代培养的分离株（命名为Grape）的4个克隆株进行基因组重测序后，未检测到任何可被识别的自发突变。该结果表明灰葡萄孢并未表现出升高的自发突变率。后续研究将帮助我们验证该遗传多样性是否、以及如何参与调控该病原体的广谱宿主侵染特性。