Biology subjects

Wyler, M.

Publications and source records attributed to Wyler, M..

13 recordsLinked to original sources

bioRxiv2026

Silent travelers: the potential of migratory birds and their ticks to introduce emerging viruses into Switzerland

Switzerland hosts over 400 bird species, many of which are migratory. Through diverse movement patterns, ranging from short distances to almost global migrations, these birds can introduce zoonotic viruses, such as West Nile virus (WNV) or avian influenza virus (AIV), as well as unknown and potentially emerging viruses. Furthermore, they facilitate the global dispersal of infected ectoparasites, particularly ticks, risking the introduction of novel tick-borne diseases. To assess this risk, we sampled 42 bird species (39 migratory, 3 resident) over seven months in 2023 at the Bolle di Magadino nature reserve and the Piano di Magadino area in the canton Ticino (Switzerland). This region, because of its transitional climate, serves as an important resting and breeding ground for migratory birds. In total, 496 oropharyngeal-cloacal swabs, 164 sera, and 22 associated ticks were collected. While RT-qPCR of the swabs detected no active WNV or AIV infections, ELISA testing identified Orthoflavivirus antibodies in 15 of 164 sera, indicating prior exposure. Metagenomic next-generation sequencing revealed a viral landscape spanning 33 families (29 of which were identified in birds). Within this virome, DNA viruses, predominantly Circoviridae, Genomoviridae, and Parvoviridae, dominated in abundance but exhibited low diversity. In contrast, the highly diverse RNA virome primarily reflected the birds dietary habits and the local habitat at the nature reserve. Notably, we report the first detection of Bole tick virus 4 (BoTV4) in Switzerland, identified in several ticks (Rhipicephalus turanicus) associated with long-distance migrants. This member of the newly established Pestiviridae family is already established in parts of Asia, Africa, and Europe. This study provides the first active surveillance of the wild bird virome in Switzerland. Our findings establish a framework for the early detection of emerging viruses and underscore the role of migratory birds as dispersal vectors for ticks and novel tick-borne viruses.

genomics↗

bioRxiv2026

Bovine-derived influenza A virus (H5N1) shows efficient replication in well-differentiated human nasal epithelial cells without requiring genetic adaptation

Highly pathogenic avian influenza (H5N1) viruses of clade 2.3.4.4b have caused significant losses among bird populations worldwide and have repeatedly crossed the species barrier, infecting mammals, including humans. However, efficient human-to-human transmission has not yet been observed. Here, we demonstrate that an H5N1 virus isolated from bovine milk in Texas in 2024 (H5N1Tex/24) replicates in differentiated human nasal epithelial cells as efficiently as a 2009 pandemic H1N1 virus strain (H1N1HH4/09) at both 37 {degrees}C and 33 {degrees}C. The adaptive mutations PB2-M631L and PA-K497R do not affect H5N1Tex/24 replication at 37 {degrees}C but promote replication at 33 {degrees}C. Conversely, H5N1BE/22, a virus from the same clade isolated from a pelican in 2022 that lacks these mutations, replicates in human nasal epithelial cells at 37 {degrees}C as efficiently as H5N1Tex/24 but exhibits limited replication at 33 {degrees}C. Introducing the two mutations PB2-M631L and PA-K497R did not overcome this limitation. Furthermore, nasal epithelial cells express receptors for both human and avian influenza viruses. Accordingly, no mutations were detected in HA which are known to switch receptor preference. Finally, we demonstrate that H5N1Tex/24 remains sensitive to the antiviral effects of interferon-{lambda} (IFN-{lambda}), however, infected nasal epithelial cells secrete only small amounts of this cytokine. Overall, our results suggest that H5N1Tex/24 possesses intrinsic traits enabling efficient replication in the human upper airways.

microbiology↗

bioRxiv2025

Systematic Discovery and Design of Synthetic Immune Receptors in Plants

Plants deploy a diverse array of pattern recognition receptors (PRRs) that perceive microbe-associated molecular patterns (MAMPs) to activate immune responses. Leucine-rich repeat receptor-like kinase subgroup XII (LRR-RLK-XII) represents one of the largest PRR families due to lineage-specific diversification. Bioinformatics, synthetic biology, and biochemical approaches were integrated to characterize PRRs from 285 plant species. We identified a receptor, named "SCORE", that perceives cold-shock protein (CSP) peptides. SCORE orthologs from multiple angiosperm lineages exhibit remarkable CSP recognition polymorphisms, indicating recurrent selection for pathogen recognition through substitutions at key amino acid residues. Through functional phylogenomics and protein structure predictions, we generated synthetic SCORE variants capable of detecting multiple phytopathogen CSP peptides, thus revealing the diverse PRR recognition landscape in plants. Our strategy hold promises for engineering plant immune receptors, particularly for perennial crops.

plant biology↗

bioRxiv2024

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates

Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winners strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams methods included quantitative genetics, classical machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.

genetics↗

bioRxiv2023

Evolutionary Trajectory of Pattern Recognition Receptors in Plants

Plants perceive pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors (PRRs) to activate PRR-triggered immunity (PTI). Despite extensive research on PTI in model plant species, the evolutionary trajectory and emergence of PRRs remain elusive. Here we conducted a comparative genomic analysis of cell-surface receptors and downstream signalling components among 350 plant species. Our findings reveal that cell-surface receptors comprise two major classes, receptor-like proteins (RLPs) and receptor-like kinases (RLKs), with RLP being more ancient whereas RLK families have undergone significant expansion. We also demonstrate that multiple downstream signalling components have an ancient origin within the plant lineage. To shed light on the immune-specificity of PRRs, we traced the evolutionary origin of immune-specific leucine-rich repeat-RLPs (LRR-RLPs) in plants. Surprisingly, we discovered that the last four LRR motifs crucial for co-receptor interaction in LRR-RLPs are closely related to those of the LRR-RLK subgroup Xb, which primarily governs growth and development. Functional characterisation further reveals that LRR-RLPs initiate immune responses through their juxtamembrane and transmembrane regions, while LRR-RLK-Xb members regulate development through their cytosolic kinase domains. Our data suggest modular evolution of cell-surface receptors in which immunity- and development-specific cell-surface receptors share a common origin. After diversification, their ectodomains, juxtamembrane, transmembrane, and cytosolic regions have either diversified or stabilised to recognize ligands that activate different downstream responses. We propose that cell-surface receptors and downstream signalling components are ancient, and likely predate the emergence of land plants, subsequently evolving to exhibit greater complexity and specificity within the land plant lineage.

plant biology↗

bioRxiv2022

Potential impact of TE-derived sRNA on gene regulation in the grassBrachypodium distachyon

In plants, the transcriptional and post-transcriptional repression of TEs involved the production of small interfering RNAs (siRNAs) that guide the de novo methylation and transcriptional silencing of TEs. Because siRNAs act via sequence complementarity, they indiscriminately target TEs and possible non-TE transcripts. TEs and their derived siRNAs might thus provide a reservoir for long-distance gene regulation. To test this hypothesis, we infected Brachypodium distachyon with Mangnaporte oryzae, the agent of Rice Blast. The infection caused the differential expression of multiple TE copies as well as a global change in gene expression. By sequencing the small RNA fraction, we identified TE-derived sRNA that are identical in sequence to motifs contained in the UTR region of differentially expressed genes. Our study opens new avenues of research to further investigate to what extent TEs may serve as a source for in trans gene regulation.

genomics↗

bioRxiv2022

Concerted expansion and contraction of immune receptor gene repertoires in plant genomes

Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether or not they co-evolve is unclear. Here we determined the copy numbers of cell-surface and intracellular immune receptors in 208 species. Surprisingly, these receptor gene families contract and/or expand together in plant genomes, suggesting the mutual potentiation of immunity initiated by cell-surface and intracellular receptors is reflected in the concerted co-evolution of the size of their repertoires across plant species.

plant biology↗

bioRxiv2021

The UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME1 For Plant Survival Under Sunlight In The Field

As sessile organisms, plants are subjected to fluctuating sunlight including potentially detrimental ultraviolet-B radiation (UV-B). In Arabidopsis thaliana, experiments under controlled conditions have shown that UV RESISTANCE LOCUS 8 (UVR8) controls photomorphogenic responses for acclimation and tolerance to UV-B; however, its long-term impacts on plant performance remain poorly understood in naturally fluctuating environments. Here we quantified the survival and reproduction of different Arabidopsis mutant genotypes in diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type in growth chambers with artificial low UV-B conditions but not in natural field conditions. Importantly, independent double mutants of UVR8 and the blue-light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. UV-B attenuation experiments in field conditions and supplemental UV-B in growth chambers demonstrated that UV-B caused the conditional cry1 uvr8 lethality phenotype. RNA sequencing in different conditions revealed a large number of genes with statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. Among them, Gene Ontology analysis identified enrichment of categories related to UV-B response, oxidative stress, photoprotection and DNA damage repair. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with CRY1, and provides an integral picture of gene expression associated with plant environmental responses under diverse environmental conditions.

plant biology↗

bioRxiv2021

Perception of a conserved family of plant signalling peptides by the receptor kinase HSL3

Plant genomes encode hundreds of secreted peptides; however, relatively few have been characterised. We report here an uncharacterised, stress-induced family of plant signalling peptides, which we call CTNIPs. Based on the role of the common co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) in CTNIP-induced responses, we identified the orphan receptor kinase HAESA-LIKE 3 (HSL3) as the CTNIP receptor via a proteomics approach. CTNIP binding, ligand-triggered complex formation with BAK1, and induced downstream responses all involve HSL3. Notably, the HSL3-CTNIP signalling module is evolutionarily ancient, predating the divergence of extant angiosperms. The identification of this signalling module will help establish its physiological role and provides a resource to understand further receptor-ligand co-evolution.

plant biology↗

bioRxiv2021

Standing genetic variation of the AvrPm17 avirulence gene in powdery mildew limits the effectiveness of an introgressed rye resistance gene in wheat

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable - a phenomenon that remains poorly understood as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used QTL mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of re-occurring gene conversion events and are members of a mildew sub-lineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sub-lineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangle complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations becomes an integral part of introgression breeding to ensure effective and durable resistance in wheat. Significance StatementDomesticated and wild wheat relatives provide an important source of new immune receptors for wheat resistance breeding against fungal pathogens. The durability of these resistance genes is variable and difficult to predict, yet it is crucial for effective resistance breeding. We identified a fungal effector protein recognised by an immune receptor introgressed from rye to wheat. We found that variants of the effector allowing the fungus to overcome the resistance are ancient. They were already present in the wheat powdery mildew gene pool before the introgression of the immune receptor and are therefore responsible for the rapid resistance breakdown. Our study demonstrates that the effort to identify new resistance genes should be accompanied by studies of avirulence genes on the pathogen side.

plant biology↗

bioRxiv2020

Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics - and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.

evolutionary biology↗

bioRxiv2020

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon.

Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon. Significance statementTransposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.

genomics↗

bioRxiv2019

Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon

O_LITransposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.\nC_LIO_LIHere we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grass Brachypodium distachyon.\nC_LIO_LIWe find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.\nC_LIO_LIOur study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.\nC_LI

genomics↗