Cronartium x flexili: Detection of interspecific F1 hybrids reveals frequent hybridization in tree rust pathogens

Hybridization is an important force in the evolution and adaptation of many plant-pathogenic fungi. Cronartium x flexili, an interspecific hybrid between two forest pathogens Cronartium ribicola (an invasive) and Cronartium comandrae (anative) was recently found widely distributed in national forests of Colorado and Wyoming. However, the evolutionary implications and possible adaptations of these hybrids are unknow. We examined genomic evidence of interspecific hybridization, mitochondrial inheritance, and signal of introgression in hybrids. We generated whole-genome sequencing of 15 C. comandrae, 44 C. ribicola and 20 C. x flexili isolated from limber and lodgepole pines during 2019 - 2021 in Colorado and Wyoming. Reads were aligned to the C. ribicola reference genome and variants were identified. Hybrids were intermediately placed between the parents, C. comandrae and C. ribicola, in phylogenetic and principal component analyses. Analysis of mitochondrial DNA from hybrids revealed that hybrids inherited mitochondria of C. ribicola. We further analyzed for the signal of introgression in hybrids by identifying ancestry- informative markers, calculating hybrid index, and heterozygosity using triangulaR. All hybrids were almost exclusively heterozygous and had a hybrid index of 0.5 indicating that the hybrids are an interspecific F1 cross. Our findings provide direct evidence of interspecific hybridization between native and invasive tree rust pathogens. More data is needed to determine the long-term ecological effects this hybrid on forest ecosystem health.