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Poster

Session: Session 1 Presenting Authors at Posters (Evens)

P-286 - Haplotype-phased genome assemblies of global barley leaf rust (Puccinia hordei) isolates reveal evidence of somatic hybridisation, repeat element expansion and structural rearrangement

Tuesday, July 15, 2025
09:55 - 11:30  
Location: Confex Hall 3
Population Biology, Ecology & Genomics

The development of haplotype-phased, dikaryotic Puccinia genomes marks a significant step forward in the surveillance and management of cereal rust pathogens. Barley leaf rust, caused by Puccinia hordei (Ph), can cause dramatic yield losses (60% reported) and reduced malting quality in temperate growing regions worldwide. To address the lack of high-quality genomic resources, PacBio HiFi and Hi-C sequencing were used to generate chromosome-length assemblies for ten global Ph isolates. These included six U.S. isolates (from CA, MN, VA, TX, and two WA) and one isolate each from China, Germany, Israel, and the Netherlands. A de novo reference genome for the U.S. isolate 17MN32B was assembled based on synteny with the haplotype-phased P. graminis f. sp. tritici isolate Pgt21-0, which then guided the scaffolding of the remaining isolates (9/10 with ≥34/36 telomeres). Nuclear genome sizes ranged from ~140–147 Mb, except for an Israeli isolate ISR90-3 (~163 Mb). Haplotype containment analyses revealed multiple somatic hybridization events shaping global Ph lineages. Ph genomes exhibited a higher repeat content (~70%) than related haplotype-phased cereal rust fungi, with expansions in LTR retroelements and DNA transposons. Additionally, putative reciprocal translocations were observed in four isolates. Evidence-based gene annotation was performed using germinated spore and infection RNAseq data from an isolate with near-universal avirulence on barley leaf rust differential lines.