Wheat and barley stripe rust pan-genome facilitates discovery of the predominant North American lineage’s origin in somatic hybridization

Wheat and barley stripe rust, caused by Puccinia striiformis formae speciales tritici ( Pst ) and hordei ( Psh ) respectively is a perennial and endemic threat to those crops worldwide. Outside the Himalayan region the fungus has not been observed reproducing sexually, despite being characterised extensively over the past 100 years by researchers in many countries. Scientific literature divides P. striiformis into lineages termed PstS0, PstS1, up to PstS18. Here we describe the first North American P. striiformis pan-genome, comprising 24 Pst and 3 Psh genomes from North America including five phased assemblies using chromosome conformation capture to separate two haploid genomes. We identify the origin of the predominant North American Pst lineage; PstS18, as a somatic hybridization event between PstS1 and another unknown lineage. As well as identifying gene families which distinguish haplotypes on a trans-lineage and trans-species level, we also show ongoing gene family loss and expansion in clonal lineages after their emergence.