Biology subjects

Kaiser, B. N.

Publications and source records attributed to Kaiser, B. N..

3 recordsLinked to original sources

bioRxiv2026

Global population genomics and pangenome of the clubroot pathogen link clonal expansion and effector diversification to resistance breakdown in canola

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae, threatens Brassica crops worldwide. Novel pathogen virulence frequently breaks resistance in agricultural crops, and yet explanations for isolate evolution remain unknown. We combined whole genome sequencing of 192 isolates from 24 countries with a pangenome analysis of 55 high-quality complete or nearly complete genome assemblies and performed functional effector analyses to investigate potential mechanisms of virulence emergence. Three major phylogenetic clusters were identified, including two highly clonal lineages with contrasting virulence profiles, and a genetically diverse population retaining signatures of recombination. Our findings support a model in which genome-wide purifying selection maintained core genome integrity, while effector genes evolved under less constraint. Despite a compact closed pangenome, we identified chromosome 17 as a major hotspot of single nucleotide and structural variations, transposable elements and expansion of ankyrin repeat effectors. Within the variable chromosome 17, PbAnk2 alleles from virulent and avirulent isolates encoded proteins with distinct predicted structures. PbAnk2 interacted with the Arabidopsis co-chaperone DJC31 in yeast two-hybrid and BiFC assays, whereas co-immunoprecipitation did not detect an interaction for the allele found in isolates that break CRa-mediated resistance, suggesting that allelic variation may alter PbAnk2's association with DJC31. These findings reveal the clonal expansion of virulent isolates and connect it to effector diversification that led to resistance breakdown and establish a genomic framework for pathogen surveillance and durable clubroot resistance.

genomics↗

bioRxiv2026

Direct effector recognition by a tandem kinase triggers non-canonical immunity in wheat

Tandem kinase proteins (TKPs) are an important class of disease resistance genes in cereal crops alongside nucleotide-binding (NB-ARC) leucine-rich repeat (LRR) (NLR) receptors. Here, we cloned the wheat (Triticum aestivum) resistance gene Lr41, which encodes a TKP with a C-terminal fusion, and its paired effector gene AvrLr41 from the rust pathogen Puccinia triticina. AvrLr41 is unusually large and highly divergent from most fungal effectors and is directly recognized by Lr41 through its pseudokinase domain. Immune activation mediated by Lr41 require auxiliary helper proteins, including either a minimal coiled-coil (CC) helper protein or its full-length NLR ortholog. These findings reveal a non-canonical immune system in which a kinase-type receptor directly recognizes an effector and recruits either CC or NLR helpers, demonstrating that full-length NLRs are not strictly required for NLR-linked immune execution and expanding the functional repertoire of disease resistance proteins in crops.

plant biology↗

bioRxiv2025

Phylogenomics and effector analysis of Plasmodiophora brassicae genomes unveils a unique and highly divergent clade in Australia

Clubroot, caused by the protist pathogen Plasmodiophora brassicae, is a soilborne disease that leads to significant yield losses in a broad range of brassica crops worldwide. Despite its significant impact on agriculture, genomic and molecular studies of clubroot disease are hindered due to the complex life cycle and the obligate biotrophic nature of the pathogen, which prevents its cultivation in vitro. In addition, several genotypes of P. brassicae are often present as a mixture in a single field sample, making it challenging to resolve high-quality assemblies of individual genomes. Recently, several genomes were assembled for some strains of P. brassicae, however, in-depth genomic analysis of this devastating pathogen remains limited. In this study, we generated complete telomere-to-telomere genome assemblies for three Australian P. brassicae field isolates using PacBio Revio HiFi sequencing combined with chromatin conformation capture technology (Hi-C). Importantly, we could generate two nearly fully phased haplotype genome assemblies from one of the field isolates. Additionally, we sequenced 14 isolates of P. brassicae, sampled from a wide geographical range across Australia using Illumina technology and performed an in-depth global comparative phylogenetic analysis. We revealed that Australian isolates are classified into three different clades, including a highly divergent and unique clade present only in Australia. Comparative analysis showed that the predicted effector profile of the Australian-unique clade is distinct from other clades, further supporting phylogenetic divergence. Altogether, we demonstrate the first haplotype-resolved genome of Australian P. brassicae isolates from a single clubroot field sample, and provide an in-depth phylogenetic analysis of global and Australian isolates. These findings, together with core effector profile analysis, will further advance the research to combat this destructive pathogen.

genomics↗