Data from: 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.

病原菌体内的现存遗传变异（standing genetic variation）如何促成宿主-病原菌互作的多样性，目前仍未得到充分阐释，部分原因在于多数研究中的病原菌均为宿主特异性的无性繁殖生物，这一特性使得遗传分析工作变得复杂。与之形成对比的是，灰葡萄孢（Botrytis cinerea）是一种可侵染多种不同植物宿主的有性繁殖型真正单倍体子囊菌（ascomycete）。尽管已有研究在两株分离株（isolate）间发现了显著的基因组差异，本研究仍着手评估灰葡萄孢种群中现存遗传变异的水平与发生频率。为了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，并将测序结果与此前已测序的T4参考基因组（reference genome）进行比对。此外，我们还对其中一株分离株的4份独立重复培养物进行了重测序。13株分离株中检测到了高水平的遗传多样性。在这些遗传变异中，我们鉴定到了一批携带效应显著多态性位点（polymorphism）的基因簇——即那些可导致预测性功能敲除的多态性位点——它们围绕在参与调控营养体不亲和性（vegetative incompatibility）的基因周围。这些基因座（locus）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，证明这些基因座确实调控营养体不亲和性。这表明灰葡萄孢体内的营养交配基因座与遗传多样性升高的基因组区域存在关联。我们对一株来源于葡萄的分离株的4份克隆（clone）进行了基因组重测序，该分离株已被独立传代培养十余年，结果未检测到任何可辨识的自发突变（spontaneous mutation）。这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探明该遗传多样性是否以及如何促成该病原菌宽广的宿主范围。