Björn Usadel

Summary: Host genetic diversity shapes pathogen susceptibility within plant populations, raising the question of whether beneficial root microbes can buffer these differences. The fungal root endophyte Serendipita indica ( Si ) promotes plant growth and can mitigate disease caused by the pathogen Bipolaris sorokiniana ( Bs ). Here, we assessed how natural host genetic variation influences Si ‐mediated protection against Bs in Arabidopsis thaliana . We screened 47 A. thaliana accessions for susceptibility to Bs with and without Si colonization and performed phenotypic, transcriptomic, and comparative genomic analyses of two genetically and geographically proximate Swedish accessions, T510 and T530, that differed strongly in Bs colonization. Si conferred consistent protection against Bs across all accessions, despite variation in baseline susceptibility and immune‐gene content. T510 and T530 differed in Bs colonization, disease symptoms, transcriptional responses, and immune‐gene repertoires, including presence–absence variation of the TIR‐NLR gene ISI . T530 lacks ISI , and mutation of ISI in Col‐0 increased Bs susceptibility, demonstrating that ISI contributes to root immunity. However, Si ‐mediated protection was retained in the absence of ISI , demonstrating that ISI is not required for this protective effect. Beneficial fungal endophytes can thus buffer phenotypic consequences of natural variation in pathogen susceptibility, stabilizing disease outcomes across genetically diverse plant populations.

Motivation: Functional regulatory variants are important determinants of heritable diversity, yet their systematic identification requires both genome-wide maps of transcription factor (TF) occupancy and suitable genome sequences for mapping. While chromosome-scale assemblies remain costly for large association panels, short-read sequencing data are widely available. We investigated whether draft genomes reconstructed from short reads are sufficient for comparative MOA-seq analyses of TF occupancy. Results: We generated genome-wide TF footprint maps for the barley cultivars Bowman, Morex, and Golden Promise, identifying approximately 240,000 loci per genotype. Roughly half of all footprints occurred in intergenic regions. Footprints conserved between genotypes were depleted for sequence variation and located closer to genes. Meanwhile, genotype-specific footprints were enriched for SNP-containing and gene-distal regions, highlighting the extensive diversity of regulatory landscapes among barley cultivars. We further compared two short-read-based draft genome assembly strategies: i) a SNP-replacement and ii) a Practical Haplotype Graph (PHG)-based composite genome approach, to enable MOA-seq analyses without chromosome-scale genome assemblies. Compared to the SNP-replacement strategy, the composite genome displayed 2.3-fold higher local sequence concordance for SNPs/INDELs relative to the published reference. Both draft genomes accurately reproduced MOA-seq profiles, recovering approximately 80 % of reference peak bases with per-base coverage correlations of 0.79–0.90 relative to the assembled reference. While the composite genome performed best across the genome overall, the simpler SNP-replacement strategy more accurately recovered TF occupancy within regulatory peaks due to fewer structural alignment artefacts. Availability: Pipelines consist of existing open-source tools, Bash, GAWK and Java, and are available at [zenodo; tbd].

Lichens are stable multipartite symbioses in which a fungal mycobiont associates with one or more photosynthetic partners while hosting complex microbiomes. Secreted antimicrobial proteins (AMPs) have recently emerged as important mediators of fungal interactions with surrounding microbial communities, yet their evolutionary distribution and diversity in lichen-forming fungi remain largely unexplored. Here, we predicted AMP repertoires across 80 phylogenetically diverse lichen-forming fungi representing three photobiont association types. Contrary to our expectation, average repertoire size did not differ between chlorolichens, cyanolichens and tripartite lichens (363 AMPs per species overall), even though repertoire size varied almost five-fold among species and 23 AMP families showed photobiont-associated enrichment or depletion. This quantitative conservation masks extensive compositional turnover, with families occurring in at least 90% of species coexisting alongside numerous lineage-specific groups. Pooled population sequencing of 11 Umbilicaria phaea populations along two elevational gradients further revealed recurrent AMP presence– absence variation within a single species. In contrast to AMPs, biosynthetic gene clusters (BGCs) and carbohydrate-active enzymes (CAZymes), which include known antimicrobials, were markedly reduced in cyanolichens relative to chlorolichens. Lichen-forming fungi thus combine a conserved baseline antimicrobial protein capacity, whose composition nonetheless turns over between lineages and populations, with chemical and enzymatic systems that differentiate along photobiont association and may support ecological and lifestyle-associated adaptation. SIGNIFICANCE STATEMENT: Lichen-forming fungi interact simultaneously with photosynthetic partners and diverse microbial communities, yet how their antimicrobial capacity evolves in this complex symbiotic context is poorly understood. By comparing 80 lichen-forming fungal genomes, we show that the size of their predicted antimicrobial protein repertoires is broadly conserved across associations with green algae, cyanobacteria, or both, despite extensive turnover in the constituent protein families across lineages and populations. In contrast, carbohydrate-active enzymes and biosynthetic gene clusters vary substantially with photobiont association. These findings reveal a decoupling of antimicrobial repertoire size from repertoire composition and from other antimicrobial molecules, suggesting that distinct molecular repertoires are subject to different evolutionary constraints. Thus, lichen-forming fungi maintain a broadly conserved genomic potential for protein-based antimicrobial activity while retaining substantial molecular flexibility.

The NFDI-consortium FAIRagro has established a systematic framework for evaluating the FAIRness of Research Data Infrastructures (RDI) within the German agrosystem research landscape. While FAIR principles are widely accepted, their practical implementation by RDIs remains challenging. By operationalizing the FAIR principles into a reproducible multi-dimensional scoring methodology, this initiative addresses the critical need for a transparent and citable benchmark of RDIs that moves beyond simple compliance. This paper details the underlying assessment criteria, comprising 20 core metrics, the iterative community-driven validation process, and the integration of these metrics into the FAIRagro Search Hub. This framework evaluates RDIs, like repositories or databases, instead of sampling hosted data sets, across the four distinct categories of FAIR independently, yielding granular, pillar-specific ratings. Unlike aggregate scoring models, which can inadvertently mask technical deficiencies by averaging performance across categories, this multi-dimensional approach ensures that a repository’s distinct strengths and bottlenecks remain fully visible. Our findings demonstrate that standardized scoring not only clarifies data accessibility for users but also highlights specific operational gaps, allowing repository providers to identify precisely where the service implementation can be enhanced. By establishing this data-driven service in the agronomy domain, we provide a scalable template for the broader NFDI and EOSC ecosystems to foster a culture of excellence in research data stewardship.

Crop wild relatives are used to improve cultivated plants and precise tracking of genetic introgression requires high-quality genome assemblies. Here we present de novo genome assemblies of two wild tomato species — the broadly stress-resistant Solanum pennellii (LA0716) and the salt-resistant Solanum cheesmaniae (LA1039). The improved S. pennellii genome adds 146 Mbp to the twelve chromosomes compared with the original reference. The alignment of the new assemblies with multiple gold-standard assemblies identified shared and species-specific structural variants. Analysis of repeat content demonstrates independent explosions of Tekay retrotransposons in S. pennellii and S. peruvianum . Genome sequencing of 709 recombinant plants derived from male and female backcrosses of three different hybrids reveals higher crossover rate in female meiosis. Conserved female-enhanced recombination regions were discovered and coldspots were attributed to megabase-scale inversions and insertion-deletion polymorphisms. Our S. pennellii and S. cheesmaniae genome assemblies reveal how repeat content diverged in nature and during breeding, and uncovers how both reproductive gender and structural variants dictate recombination landscapes in tomato hybrids.

In October 2024, Parties to the United Nations Convention on Biological Diversity agreed to a new multilateral mechanism to fund biodiversity conservation through the sharing of benefits from open biodiversity data. Biological databases hosting genetic and other biological data, known as digital sequence information (DSI), are central to the implementation of the mechanism. This paper assesses the new international agreement and its implications for DSI databases. We walk through the database provisions in COP16 Decision 16/2, which include notifying users and submitters about the mechanism, improving metadata on geographical location of sample collection, and consistency with open access, as well as consideration of the FAIR, CARE, and TRUST principles. Drawing on surveys, interviews, and a workshop with biological database managers, we identify practical and scalable measures including updating terms of use, revising submission procedures, and strengthening user communication. We also propose approaches to capture and report non-monetary benefits such as capacity building, publications, interoperability, and training. These actions illustrate how DSI databases can remain open, sustainable, and globally connected while supporting benefit-sharing from the use of DSI on genetic resources.

Fungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition, extracellular signaling, nutrient exchange, immune modulation, and control of microbial competitors. In filamentous pathogens such traits are frequently associated with compartmentalized genomes, including rapidly evolving secreted proteins known as effectors and expanded receptor families, but it remains unclear whether similar genomic principles shape mutualistic fungal symbioses. Here, we generated a chromosome-scale super-pangenome for the lichen-forming genus Peltigera, comprising 41 mycobiont assemblies representing eleven species, together with genomes of associated Nostoc and, in tripartite species, Coccomyxa photobionts. The mycobiont genomes revealed extensive variation in genome size, transposable element content, biosynthetic gene clusters, and lineage-specific gene content, with pronounced expansions in tripartite species. Across Peltigera, secreted protein encoding genes were preferentially located in TE-rich regions. We further identified Starship-like transposon elements, expanded antimicrobial protein repertoires, and a large, previously underestimated repertoire of fungal GPCRs dominated by Pth11-like receptors. Layer-specific transcriptomics of a P. rufescens thallus showed differential expression of several interaction-associated gene families, e.g. lectins, antimicrobial proteins and Pth11-like GPCRs. These data indicate that pathogenic and mutualistic fungi might exhibit shared genomic principles, including genome compartmentalization, mobile-element-associated diversification, and the expansion of molecular repertoires involved in recognition, extracellular control and signaling.

In plant sciences, single-cell and spatial transcriptomics generate large complex datasets which require structured metadata in order to make them interoperable and reproducible. In this work, we demonstrate how the Annotated Research Context (ARC) can be used for the management of such data using a barley single-cell RNA sequencing dataset integrated with spatial transcriptomics data. Experimental metadata was captured in ISA tables using ontology annotations to ensure machine readability and interpretability. The computational analyses were wrapped as Common Workflow Language (CWL) scripts to ensure reproducibility of the results and reusability of both the data and the analysis pipeline. The ARC links input materials unambiguously to the analysis results, allowing the research community to trace the entire investigation procedure. Our use case shows the benefits of using an ARC for structuring and annotating heterogeneous data, enabling comparative analyses across different datasets. While wrapping analysis scripts with CWL required some technical knowledge, the resulting standardized and reusable workflows outweigh this entry barrier. Parameter variations can be easily tested and results linked correctly without manual editing of the workflows themselves. Overall, this work highlights how using the ARC framework for single-cell datasets improves the FAIRness of the data and increases the reusability.

Motivation: Trimmomatic is a widely adopted tool for preprocessing high-throughput sequencing data, particularly from Illumina platforms. Since its original publication in 2014, the volume and complexity of sequencing data have increased dramatically, necessitating continuous tool evolution. Results: We present the substantial updates to Trimmomatic over the past decade. Key enhancements include a robust multithreading model for high-performance parallel processing, parallel GZIP/BZIP2 compression, and a suite of new trimming and filtering steps to provide users with more flexible quality control. Usability has been significantly improved through automatic PHRED encoding detection and simplified file handling. The codebase has also been modernized including Maven support, and continuous integration to ensure long-term sustainability and community contributions. These updates solidify Trimmomatic’s role as an efficient, flexible, and essential tool in modern bioinformatics pipelines. Availability: Trimmomatic remains open-source under the GPL V3 license, with the latest version available at https://github.com/usadellab/Trimmomatic and also on our website https://www.plabipd.de/trimmomatic_main.html (DOI: https://doi.org/10.5281/zenodo.18678155).

Electronic laboratory notebooks (ELNs) are widely used in the life sciences, but their notebook format limits machine-readability and FAIR compliance. Consequently, researchers often spend significant manual effort restructuring ELN records into publication-ready outputs. We present elab2ARC, a browser-based workspace that automates the conversion of open-source eLabFTW records into Annotated Research Contexts (ARCs) - version-controlled, ISA-compliant research objects. Using the eLabFTW API, elab2ARC retrieves administrative metadata, protocols, and attachments, reorganising them into ISA-compliant tables and linked datasets. All processing occurs client-side, ensuring user data control before submission to the PLANTdataHUB repository. An optional LLM-assisted workflow extracts structured metadata from free-text protocols, providing editable drafts while preserving human oversight. Designed for use at project completion, elab2ARC reuses existing ELN documentation without disrupting daily laboratory practice. It offers a practical route to FAIR-aligned sharing, publication, and long-term archiving of life-science experimental records.