Genomewide mutation dynamic within a long-lived individual of Armillaria gallica

Mutation is the ultimate source of all genetic variation in populations and yet they remain unobservable and buried in the past. Long-lived individuals of Armillaria gallica, a common opportunistic fungal pathogen of tree roots in temperate forests of the northern hemisphere, provide a spatial context for examining the mutational dynamic. Each individual of A. gallica arises in a single mating between two haploid gametes and the resulting diploid then grows vegetatively to occupy a discrete spatial territory often including many adjacent tree root systems. In effect, this leaves a spatial record of growth over time within which mutations can be localized. To identify mutations, the entire genomes of three spatially separated samples of one individual of A. gallica approximately 200 × 60 m were sequenced and compared. In this comparison, mutations and regions of loss of heterozygosity (LOH) were identified then assayed in another 20 isolates from the same individual by conventional PCR and Sanger sequencing. The genotype network of all mutations and LOH were without internal conflict. Further, the spatial pattern of genotypes was nonrandom and appeared to reflect the vegetative expansion leading to the present-day individual. The results reflect the spectrum of spontaneous mutation in nature and provide insight into cellular generation times.