Biology subjects

Skiadas, P.

Publications and source records attributed to Skiadas, P..

5 recordsLinked to original sources

bioRxiv2025

Evolution of resistance breaking in spinach downy mildew revealed through pangenome graph analysis

BackgroundFilamentous plant pathogens secrete effectors to successfully establish host infections. In resistant crop varieties, plant immunity can be triggered by immune receptors that recognize these effectors. Resistant crop varieties are grown in large-scale monocultures imposing strong selection pressure on pathogens, driving rapid evolution of effector repertoires resulting in the frequent breakdowns of resistance within just a few growing seasons. The oomycete Peronospora effusa, responsible for downy mildew on spinach, is an example of a rapidly adapting pathogen, but it is yet unknown how P. effusa can successfully overcome resistance of spinach by genomic adaptations. ResultsTo close this knowledge gap, we here generated genome assemblies and constructed a pangenome graph for 19 isolates corresponding to 19 officially denominated resistance-breaking P. effusa races, which can cause disease on a differential set of spinach cultivars. Haplotype-resolved pangenome graph analyses revealed that many isolates emerged from recent sexual recombination, yet others evolved via prolonged asexual reproduction and loss of heterozygosity. By phasing effector candidates to determine their allelic variation, we identified effector candidates associated to resistance breaking of spinach varieties and reconstructed the evolutionary events that led to their diversification. ConclusionsThe here developed and applied computational genomics approaches offer unparalleled insights into the molecular mechanisms of the rapid evolution of P. effusa, and points to potential targets for future resistance breading.

genomics↗

bioRxiv2024

Exploiting Pseudomonas syringae Type 3 secretion to study effector contribution to disease in spinach

Intensive spinach cultivation creates favourable conditions for the emergence and rapid evolution of pathogens, leading to substantial economic losses. Research on host-pathogen interactions in leafy greens would benefit from advanced biotechnological tools, however absence of such tools in spinach hampers our understanding of spinach immunity. Here, we explored the potential of Type III Secretion System (T3SS)-mediated effector delivery to study pathogen effector activity in spinach. We identified the Pseudomonas syringae pv. tomato DC3000 (DC3000) polymutant D36E, which lacks 36 known T3SS effectors (T3Es), as a promising T3SS-dependent effector delivery system for spinach. Unlike DC3000, which causes necrotic symptoms on spinach and reaches high bacterial titres, D36E did not proliferate and caused no visible symptoms. Using D36E, we screened 28 DC3000 T3Es in spinach, assessing symptom development, bacterial proliferation, and reactive oxygen species (ROS) bursts as a proxy for early immune responses. AvrE1 and HopM1 emerged as key determinants of DC3000-like infection, inducing water-soaked lesions, while HopAD1 strongly suppressed ROS production. Our findings establish the D36E-based effector delivery system as a powerful tool for high-throughput effector studies in spinach. It bridges the gap between genomics-based effector predictions and experimental validation, paving the way for knowledge-driven resistance breeding in non-model crops like spinach.

plant biology↗

bioRxiv2024

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage and expand on an innovative, multi-genome method to construct, annotate, and analyse the first pangenome graph of an oomycete plant pathogen. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, pathogenicity related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens. Author SummaryPlant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen.

genomics↗

bioRxiv2023

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

Bacteriophages are important drivers of microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. To address this gap, we analyzed viral dynamics across 20 compost-derived microbial communities propagated for one year in mesocosms. Communities clustered into two distinct types, each dominated by different cellulose-degraders and comprising hundreds of genera. In one type, we observed massive, parallel outbreaks of Theomophage, a previously undescribed bacteriophage, reaching 74% of metagenomic sequencing reads, the largest bacteriophage outbreak documented to date. Theomophage populations in isolated communities were composed of a single genotype that showed striking evolutionary stability throughout the experiment. In contrast, following experimental viral migration between mesocosms, all Theomophage populations showed rapid evolution via recombination between preexisting genotypes, replacement of ancestral lineages, and, upon successful migration to mesocosms of the alternate community type where Theomophage was initially absent, rapid acquisition of novel mutations that swept local populations and then spread to other mesocosms. Our study reveals the spatial and temporal scales at which bacteriophage microdiversity evolves in complex communities. It further shows that mixing of viral communities -- likely common in natural systems -- can rapidly accelerate bacteriophage evolution.

microbiology↗

bioRxiv2021

Sexual reproduction contributes to the evolution of resistance breaking isolates of the spinach pathogen Peronospora effusa

Peronospora effusa causes downy mildew, the economically most important disease of cultivated spinach worldwide. To date, 19 P. effusa races have been denominated based on their capacity to break spinach resistances, but their genetic diversity and the evolutionary processes that contribute to race emergence are unknown. Here, we performed the first systematic analysis of P. effusa races showing that those emerge by both asexual and sexual reproduction. Specifically, we studied the diversity of 26 P. effusa isolates from 16 denominated races based on mitochondrial and nuclear comparative genomics. Mitochondrial genomes based on long-read sequencing coupled with diversity assessment based on short-read sequencing uncovered two mitochondrial haplogroups, each with distinct genome organization. Nuclear genome-wide comparisons of the 26 isolates revealed that ten isolates from six races could clearly be divided into three asexually evolving groups, in concordance with their mitochondrial phylogeny. The remaining isolates showed signals of reticulated evolution and discordance between nuclear and mitochondrial phylogenies, suggesting that these evolved through sexual reproduction. Increased understanding of this pathogens reproductive modes will provide the framework for future studies into the molecular mechanisms underlying race emergence and into the P. effusa-spinach interaction, thus assisting in sustainable production of spinach through knowledge-driven resistance breeding. Significance statementMany microbial plant pathogens depend on the successful colonization of their hosts to complete their life cycle, thereby damaging food crops worldwide. The most effective way of disease control is to deploy genetic disease resistances. However, the extensive use of resistant crop varieties exerts strong selective pressure on microbial plant pathogens to adapt in order to escape resistance. Through yet unknown mechanisms, the spinach pathogen Peronospora effusa can rapidly break the resistance of newly introduced varieties, often within a single growing season. Thus, there is an urgent need to better understand the mechanisms driving adaptation in P. effusa. This information will lead the way to knowledge-driven resistance breeding. Here, we capture for the first time the genetic variation of 26 P. effusa, 16 of which can break a different combination of host resistances. We demonstrate that P. effusa isolates evolve by both asexual and sexual reproduction, and thereby provide the framework to study the molecular mechanisms of the interactions between P. effusa and spinach.

evolutionary biology↗