Samuel.holden@ubc.ca, meng.li@botany.ubc.ca, Mehrdad.abbasi@ubc.ca, david.kim2@agr.gc.ca, sean.formby@gmail.com, sean.walkowiak@grainscanada.gc.ca, guus.bakkeren@agr.gc.ca, gurcharn.brar@ualberta.ca.

Biotic stressors such as pathogens can jeopardize global food security. When considering the wheat rust diseases (stripe, stem, and leaf rust), the largest threat to production comes from the emergence of new, highly virulent pathogen strains as exemplified by the 2015 ‘Warrior’ epidemic in Europe, and the ongoing spread of Ug99 across Africa.

We take advantage of recent advances in sequencing technology and field pathogenomics which have made it viable to monitor the population dynamics of wheat rusts through sampling and genotyping field populations to assemble the genomes of over 20 isolates of Puccinia striiforimis f. sp. tritici (Pst, the causal pathogen of wheat stripe rust), including PacBio HiFi and HiC assembly of four fully phased genomes which account for each of the two haploid nuclei (the dikaryons) present in a rust colony; developing the first field pan-genome of Pst.

By comparing representatives of the major lineages present in North America, we used these data to demonstrate that the Pst18 lineage which has become dominant in North America, supplanting the older PstS1 lineage shares a single haploid nuclear genome with PstS1; indicating that the two are related through somatic hybridization with a third, unknown, lineage.

To our knowledge this marks the third conclusive demonstration of lineage emergence via somatic hybridization in the wheat rusts and the first in Pst specifically. Coupled with the mixed evidence to support ongoing sexual recombination in Pst this result has powerful implications for the emergence of novel lineages worldwide, and underscores the importance of monitoring field populations for the introduction of genetic novelty which may accompany the emergence of totally new pathogen races.