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.