Biology subjects

van Steenbrugge, J. J. M.

Publications and source records attributed to van Steenbrugge, J. J. M..

4 recordsLinked to original sources

bioRxiv2025

The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus

Globodera pallida poses a major threat to potato production, with management strategies primarily relying on genetic resistance. However, reports from multiple locations in Western Europe indicate a steady increase in virulence levels among field populations, raising major concerns about G. pallida control. The evolutionary mechanisms driving this rise in virulence are poorly understood. To investigate this, we analysed the propagation of thirteen recently isolated field populations on thirty commercial potato varieties over four independent PCN resistance tests. Our findings indicate that (1) the genetic basis of resistance in potatoes is small, with the major resistance conferred by GpaV from Solanum vernei, and (2) the wide application of GpaVvrn has led to continuous selection on standing genetic variation in G. pallida field populations. To map virulence, we propagated two field populations on a GpaVvrn-resistant variety for four consecutive generations. High-coverage whole-genome sequencing of each generation revealed that GpaVvrn-mediated selection acted on a single locus of a newly assembled G. pallida Rookmaker reference genome. Examination of this virulence-associated locus identified Gp-pat-1 as a candidate gene. Silencing Gp-pat-1 increased G. pallida virulence on a GpaVvrn-resistant potato variety but had no effect on nematode virulence on a susceptible variety. Thereby classifying Gp-pat-1 as an avirulence gene and confirming its role in the breakdown of GpaVvrn-resistance. These findings demonstrate that negative selection on the Gp-pat-1 avirulence allele by GpaVvrn-mediated resistance is driving the emergence of virulence in the G. pallida field populations used in our selection experiments. Our results therefore strongly suggest that selection on Gp-pat-1 is likely underlying the current outbreak of GpaVvrn-resistance breaking populations. Our results provide a foundation for the development of molecular diagnostic tools to monitor virulence in field populations, to enhance understanding of resistance breakdown, and to inform the sustainable deployment of resistances in the field. SIGNIFICANCE STATEMENTIn Western Europe, management of the potato cyst nematode Globodera pallida primarily relies on genetic resistances in potato plants. However, resistance-breaking populations are emerging across Western Europe. Here, we identify a single resistance locus shared by all tested resistant potato varieties. We also identify a corresponding virulence locus on a newly assembled G. pallida reference genome and identify a gene within this locus that contributes to virulence. Our findings provide critical insights into the selective pressure acting on this plant-parasitic nematode, the emergence of virulence over time, and the molecular mechanism underlying resistance breakdown. These results provide much needed insights into a highly adapted soil-borne plant-pathogen.

genetics↗

bioRxiv2021

Comparative genomics among three cyst nematode species reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs

Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are an essential handle for PCN control. However, the poor delineation of G. pallida pathotypes hampers the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCN after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ( DOG boxes) were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Re-sequencing of PCN populations with deviant virulence characteristics will allow for the linking of these characteristics with the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.

genomics↗

bioRxiv2021

The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B.

Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.

genetics↗

bioRxiv2021

Comparative Genomics of two Inbred Lines of the Potato Cyst Nematode Globodera rostochiensis reveals disparate Effector Family-specific Diversification Patterns

BackgroundPotato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these soil-borne parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is for fundamental and practical reasons barely useful. As a result, resistant potato varieties are worldwide used in a non-informed manner. ResultsWe generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a {approx} 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 18 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in immune suppression, constitute by far the most diversified family with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. ConclusionTwo novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a solid basis for an effectorome-based virulence scheme for this notorious pathogen.

genomics↗