Algaba, J. R. | bioRxiv Science

bioRxiv2026

A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

Puccinia striiformis f. sp. hordei (Psh) causes barley stripe rust, an economically important disease affecting barley production across multiple temperate regions. Unlike its well-studied wheat-infecting relative P. striiformis f. sp. tritici, genomic resources for Psh remain limited, with no fully documented chromosome-scale, haplotype-resolved reference genomes publicly available. Here we present a high-quality, haplotype-resolved genome assembly of the dikaryotic Psh isolate NP85002, generated using Oxford Nanopore long-read sequencing combined with Hi-C chromatin conformation capture. The assembly comprises 18 chromosomes per haplotype (151.3 Mb total) including 33 telomere-to-telomere chromosomes, telomeric repeats at 69/72 chromosome ends, and six internal gaps. The assembly shows high consensus accuracy (QV >72) and strong haplotype separation (97.54% within-haplotype Hi-C contacts). Genome completeness reached 90.1% complete BUSCOs, and a combined lift-over plus ab initio annotation achieved 94.4% complete BUSCOs. Repeat annotation indicates 45% repetitive content. We additionally provide a 102,058 bp mitochondrial genome assembly with 40 annotated genes. This genome resource provides a chromosome-scale framework for comparative and population genomic analyses of barley stripe rust and related cereal rust pathogens.

microbiology↗

bioRxiv2025

Long-term surveillance suggests multiple hybridization events by nuclear reassortment and accelerated intercontinental spread of wheat yellow rust

O_LIEvolutionary forces affecting crop pathogens, including hybridization and long-distance dispersal (LDD), may have strong implications for food security and sustainable plant disease control at global scales. However, consolidated evidence is often lacking due to absence of consistent pathogen surveys beyond national capacities. C_LIO_LIOur study documents world-wide connectivity between populations of Puccinia striiformis, causing yellow rust on cereals and grasses, when analysing 3240 pathogen samples collected in 41 countries on six continents from 2009-2023. Our analyses revealed twelve cases of inter-continental spread of Puccinia striiformis, including seven cases with major impact on disease epidemics in recipient areas. C_LIO_LISomatic hybridization by nuclear reassortment between co-existing multi-locus genotypes (MLGs) on a common host was the most plausible mechanism for the emergence of three novel clonal groups of global relevance, first detected in Europe. Subsequently, onwards spread to South America and Australia was observed. Several high-impact incursions from South Asia into East Africa were also observed, including a genotype with a dramatic impact on wheat breeding programs of global relevance. C_LIO_LIOur study stresses an urgent need for coordinated crop pathogens monitoring across borders. Only global efforts will enable prevention and control of pathogens that represent major challenges for food security at regional and global scales. C_LI

evolutionary biology↗