Genomic biosurveillance detects a sexual hybrid in the sudden oak death pathogen

Abstract

Invasive exotic pathogens pose a threat to trees and forest ecosystems worldwide, hampering the provision of essential ecosystem services such as carbon sequestration and water purification. Hybridization is a major evolutionary force that can drive the emergence of pathogens. Phytophthora ramorum, an emergent pathogen that causes the sudden oak and larch death, spreads as reproductively isolated divergent clonal lineages. We use a genomic biosurveillance approach by sequencing genomes of P. ramorum from survey and inspection samples and report the discovery of variants of P. ramorum that are the result of hybridization via sexual recombination between North American and European lineages. We show that these hybrids are viable, can infect a host and produce spores for long-term survival and propagation. Genome sequencing revealed genotypic combinations at 54,515 single nucleotide polymorphism loci not present in parental lineages. More than 6,000 of those genotypes are predicted to have a functional impact in genes associated with host infection, including effectors, carbohydrate-active enzymes and proteases. We also observed post-meiotic mitotic recombination that could generate additional genotypic and phenotypic variation and contribute to homoploid hybrid speciation. Our study highlights the importance of plant pathogen biosurveillance to detect variants, including hybrids, and inform management and control.

Genome-Enabled Insights into Downy Mildew Biology and Evolution

“…Population genetics studies of B. lactucae and its host exemplified the process of host-pathogen coevolution and identified the short durability of host resistance (73). Recently, the importance of biosurveillance of global populations has been shown by the study of the sudden oak death pathogen (P. ramorum) for which sexual hybrids between a North American and European lineage were recently reported in North America that may result in novel lineages of ecological consequence (51).…”

Genetic architecture of disease resistance and tolerance in Douglas‐fir trees

“…We designed an assignment procedure to test the most likely origin of the group of unknown isolates as described in Hamelin et al (2022). This procedure consisted of building a Bayesian naı ¨ve classifier model for two different classes (i.e.…”