Biology subjects

Bakkeren, G.

Publications and source records attributed to Bakkeren, G..

6 recordsLinked to original sources

bioRxiv2025

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.

microbiology↗

bioRxiv2024

A birds-eye view: exploration of the flavin-containing monooxygenase (FMO) superfamily in common wheat.

The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signalling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis- acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.

plant biology↗

bioRxiv2023

Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating-type alleles

The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst); the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level, as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the introduction of novel genetic lineages has the potential to cause serious epidemics such as the one caused by Warrior lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and origin of foreign incursions was not known. We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in a global context, origin, and evidence for foreign incursion. More importantly, for the first time ever, we identified nine alleles of the homeodomain mating-type locus in the worldwide Pst population and show that previously identified lineages generally exhibit a single pair of these alleles. In addition, we find only two pheromone receptor alleles. We show that the recent population shift from the PstS1 lineage to the PstS1-related lineage is also associated with the introduction of a novel mating-type allele (b-3) to the Canadian population. We also show evidence for high levels of mating-type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as PstPr (probable recombinant) which we identify as a foreign incursion from China circa. 2010. These data provide comprehensive details on the population biology of Canadian Pst diversity and mating-type alleles in the global Pst population which can be utilized in testing several research questions and hypotheses around sexuality and parasexuality in rust fungi.

genomics↗

bioRxiv2020

The Ustilago hordei-barley interaction is a versatile system to characterize fungal effectors

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence/pathogenicity. In this study, we present the U. hordei-barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We have generated U. hordei solopathogenic strains, which form infectious filaments without presence of compatible mating partner. Solopathogenic strains are suitable as heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization were analyzed by transmission electron microscopy, which shows that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

plant biology↗

bioRxiv2020

UhAVR1, an HR-triggering avirulence effector of Ustilago hordei, is secreted via the ER-Golgi pathway to the cytosol of barley coleoptile cells and contributes to virulence early in infection.

The basidiomycete Ustilago hordei (Uh) causes covered smut disease of barley and oats. Virulence effectors that aid the infection process and support the pathogens lifestyle have been described for this fungus. Genetically, six avirulence genes are known and one codes for UhAVR1, the only proven avirulence effector identified in smut pathogens to date that triggers complete immunity in barley cultivars carrying the resistance gene Ruh1. A prerequisite for resistance breeding is understanding the host targets and molecular function of UhAVR1. Analysis of this effector upon natural infection of barley coleoptiles using teliospores showed that UhAVR1 is expressed during the early stages of fungal infection where it leads to HR triggering in resistant cultivars or performs its virulence function in susceptible cultivars. Fungal secretion of UhAVR1 is directed by its signal peptide and occurs via the BrefeldinA-sensitive ER-Golgi pathway, both in cell culture away from its host, and during barley interaction. Transient expression of this effector in barley and a heterologous host, Nicotiana benthamiana (Nb), supports a cytosolic localization. Delivery of UhAVR1 via foxtail mosaic virus, Pseudomonas species or Agrobacterium-mediated suppression of cell inducers in barley and Nb support a role in the suppression of a common component(s) of ETI and PTI which is conserved in both plant systems.

molecular biology↗

bioRxiv2020

Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations.

BackgroundThe wheat leaf rust fungus, Puccinia triticina Erikss. is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates and to gain insight into race evolution. The collection included isolates comprising many different race phenotypes collected worldwide from common wheat in the U.S. and the European Union together with isolates from durum wheat. One isolate from the wild wheat relative Aegilops speltoides, and two from Ae. cylindrica were also included for comparison. ResultsBased on 121,907 variants identified relative to the reference race 1-1 genome, the isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in approximately 1400 secreted resistance interactor candidate proteins. In gene-coding regions, all groups had high ratios of non-synonymous to synonymous mutations and nonsense to readthrough mutations. ConclusionsBased on total variation or variation in the secreted protein genes, isolates grouped the same indicating that variants were distributed across the entire genome. Our results suggest that recurrent mutation and selection play a major role in differentiation within the clonal lineages.

genomics↗