John Paul Rathjen

The paper presents a high-quality, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei using long-read and Hi-C sequencing.

The paper tracks global spread and hybridization of wheat yellow rust pathogen, identifying nuclear reassortment and intercontinental movement as key drivers of evolution and disease impact.

The paper clones AvrYr7, an effector gene in wheat stripe rust, and identifies variants that evade recognition by the resistance gene Yr7 through sequence and expression differences.

The paper identifies an AvrPstB48 effector from stripe rust fungus that triggers defence responses in wheat but does not directly correlate with disease outcomes.

The paper uses long-read genomics to study dikaryotic fungus genome biology, revealing nuclear-specific evolution and allele-specific expression.

The paper investigates how the flax rust pathogen secretes and delivers effector proteins into host cells, finding that a specific N-terminal fragment is required for translocation into the host cell.

The paper identifies a key residue in barley Mla NLR genes that enables effector binding through in vitro shuffling and yeast-two-hybrid screening.

This study presents a chromosome-scale genome assembly of the flax rust fungus, revealing two large effector proteins, AvrM3 and AvrN, and providing insights into its mating system.

The paper compares methods for identifying fungal species from sequencing data and finds that aligning sequences to a fungi-specific database with coverage cutoffs improves accuracy.

This paper demonstrates that linked machine learning classifiers improve species classification of fungi using error-prone long-reads on extended metabarcodes, achieving high recall and low false positives.

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.

The paper presents an open-source workflow for establishing MinION long-read sequencing in any laboratory, achieving >8.5 Gb of data with mean read length 13 kb and N50 26 kb.

This study presents haplotype-phased genome assemblies of two dikaryotic Puccinia coronata f. sp. avenae isolates, revealing structural variation and heterozygous SNPs, and identifies co-expressed effector candidates associated with virulence differences.