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Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution. Analysis of genotyping-by-sequencing data for more than 20,000 barley accessions from a German genebank provides a framework for genomics-assisted genebank management and analysis of large germplasm collections for important crops.

Genebanks harbor a large treasure trove of untapped plant genetic diversity. A growing world population and a changing climate require an increase in the production and development of stress resistant plant cultivars while decreasing the acreage. These requirements for improved plant cultivars can be supported by the broader exploitation of plant genetic resources (PGR) as inputs for genomics-assisted breeding. To support this process we have developed BRIDGE, a data warehouse and exploratory data analysis tool for genebank genomics of barley ( L.). Using efficient technologies for data storage, data transfer and web development, we facilitate access to digital genebank resources of barley by prioritizing the interactive and visual analysis of integrated genotypic and phenotypic data. The underlying data resulted from a barley genebank genomics study cataloging sequence and morphological data of 22,626 barley accessions, mainly from the German Federal genebank. BRIDGE consists of interactively coupled modules to visualize integrated, curated and quality checked data, such as variation data, results of dimensionality reduction and genome wide association studies (GWAS), phenotyping results, passport data as well as the geographic distribution of germplasm samples. The core component is a manager for custom collections of germplasm. A search module to find and select germplasm by passport and phenotypic attributes is included as well as modules to export genotypic data in gzip-compressed variant call format (VCF) files and phenotypic data in MIAPPE-compliant ISA-Tab files. BRIDGE is accessible at the following URL: https://bridge.ipk-gatersleben.de.

The chromatin remodeling protein alpha thalassemia/mental retardation syndrome X-linked (ATRX) is a component of promyelocytic leukemia nuclear bodies (PML-NBs) and thereby mediates intrinsic immunity against several viruses including human cytomegalovirus (HCMV). As a consequence, viruses have evolved different mechanisms to antagonize ATRX, such as displacement from PML-NBs or degradation. Here, we show that depletion of ATRX results in an overall impaired antiviral state by decreasing transcription and subsequent secretion of type I IFNs, which is followed by reduced expression of interferon-stimulated genes (ISGs). ATRX interacts with the transcription factor interferon regulatory factor 3 (IRF3) and associates with the IFN-β promoter to facilitate transcription. Furthermore, whole transcriptome sequencing revealed that ATRX is required for efficient IFN-induced expression of a distinct set of ISGs. Mechanistically, we found that ATRX positively modulates chromatin accessibility specifically upon IFN signaling, thereby affecting promoter regions with recognition motifs for AP-1 family transcription factors. In summary, our study uncovers a novel co-activating function of the chromatin remodeling factor ATRX in innate immunity that regulates chromatin accessibility and subsequent transcription of interferons and ISGs. Consequently, ATRX antagonization by viral proteins and ATRX mutations in tumors represent important strategies to broadly compromise both intrinsic and innate immune responses.

Plant pan-genomes, which aggregate genomic sequences and annotations from multiple individuals of a species, have emerged as transformative tools for understanding genetic diversity, adaptation, and evolutionary dynamics. Super-pan-genomes, extending across species boundaries, further enable comparative analyses of clades or genera, bridging breeding applications with evolutionary insights (Shang et al., 2022; Li et al., 2023a). However, the absence of standardized practices for data generation, analysis, and sharing hinders reproducibility and interoperability. This white paper presents a harmonized framework developed by the ELIXIR E-PAN consortium, addressing nomenclature, quality control (QC), data formats, visualization, and community practices. By adopting these guidelines, researchers can enhance FAIR (Findable, Accessible, Interoperable, Reusable) compliance, foster collaboration, and accelerate translational applications in crop improvement and evolutionary biology.

Experimental data is only useful to other researchers if it is findable, accessible, interoperable, and reusable (FAIR). The ISA-Tab framework enables scientists to publish metadata about their experiments in a plain text, machine-readable format that aims to confer that interoperability and reusability. A Python software package (isatools) is currently being developed to programmatically produce these metadata files. For Java-based environments, there is no equivalent solution yet. While the isatools package provides a lot of flexibility and a wealth of different features for the Python ecosystem, a package for JVM-based applications might offer the speed and scalability needed for writing very large ISA-Tab files, making the ISA framework available in an even wider range of situations and environments. Here we present a light-weight and scalable Java library (isa4j) for generating metadata files in the ISA-Tab format, which elegantly integrates into existing JVM applications and especially shines at generating very large files. It is modeled after the ISA core specifications and designed in keeping with isatools conventions, making it consistent and intuitive to use for the community. isa4j is implemented in Java (JDK11+) and freely available under the terms of the MIT license from the Central Maven Repository ( https://mvnrepository.com/artifact/de.ipk-gatersleben/isa4j). The source code, detailed documentation, usage examples and performance evaluations can be found at https://github.com/IPK-BIT/isa4j.

The Galaxy workflow system is an open-source platform supporting data-intensive research in life sciences, featuring a user-friendly web interface for complex analyses without extensive programming. It also offers a representational state transfer based API, enabling remote execution of specific tools. Galaxy supports similarity searches for nucleotide and amino acid sequences, with integrated tools like NCBI BLAST+ and DIAMOND. However, no specialized software currently exists for convenient use of NCBI BLAST+ and DIAMOND via the Galaxy API. blast2galaxy is a Python package that uses the Galaxy API to run sequence alignments with NCBI BLAST+ and DIAMOND as Galaxy-wrapped tools on compatible servers. It includes a command-line interface that mirrors the CLI of BLAST+ and DIAMOND and a high-level Python API for direct alignments from Python applications. The package relies on bioblend for communication with the Galaxy API. blast2galaxy is available as open-source software under the MIT license. The source code is available on Github: https://github.com/IPK-BIT/blast2galaxy. It can be installed from the Python Package Index using \"pip install blast2galaxy\" or from the Bioconda channel using \"conda install -c bioconda blast2galaxy\". Docker and Apptainer images are available and referenced in the documentation which is available under https://blast2galaxy.readthedocs.io.

Plant pan-genomes, which aggregate genomic sequences and annotations from multiple individuals of a species, have emerged as transformative tools for understanding genetic diversity, adaptation, and evolutionary dynamics. Super-pan-genomes, extending across species boundaries, further enable comparative analyses of clades or genera, bridging breeding applications with evolutionary insights (Shang et al., 2022; Li et al., 2023a). However, the absence of standardized practices for data generation, analysis, and sharing hinders reproducibility and interoperability. This white paper presents a harmonized framework developed by the ELIXIR E-PAN consortium, addressing nomenclature, quality control (QC), data formats, visualization, and community practices. By adopting these guidelines, researchers can enhance FAIR (Findable, Accessible, Interoperable, Reusable) compliance, foster collaboration, and accelerate translational applications in crop improvement and evolutionary biology.

Background: The sequencing of whole genomes is becoming increasingly affordable. In this context large-scale sequencing projects are generating ever larger datasets of species-specific genomic diversity. As a consequence, more and more genomic data needs to be made easily accessible and analyzable to the scientific community. Results: We present DivBrowse, a web application for interactive visualization and exploratory analysis of genomic diversity data stored in Variant Call Format (VCF) files of any size. By seamlessly combining BLAST as an entry point together with interactive data analysis features such as principal component analysis in one graphical user interface, DivBrowse provides a novel and unique set of exploratory data analysis capabilities for genomic biodiversity datasets. The capability to integrate DivBrowse into existing web applications supports interoperability between different web applications. Built-in interactive computation of principal component analysis allows users to perform ad-hoc analysis of the population structure based on specific genetic elements such as genes and exons. Data interoperability is supported by the ability to export genomic diversity data in VCF and General Feature Format (GFF3) files. Conclusion: DivBrowse offers a novel approach for interactive visualization and analysis of genomic diversity data and optionally also gene annotation data by including features like interactive calculation of variant frequencies and principal component analysis. The use of established standard file formats for data input supports interoperability and seamless deployment of application instances based on the data output of established bioinformatics pipelines. Competing Interest Statement The authors have declared no competing interest.

Dynamic control of circular polarization in chiral metasurfaces is being used in many photonic applications. However, simple fabrication routes to create chiral materials with considerable and fully tunable chiroptical responses at visible and near-infrared wavelengths are scarce. Here, we describe a scalable bottom-up approach to construct cross-stacked nanoparticle chain arrays that have a circular dichroism of up to 11°. Due to their layered design, the strong superchiral fields of the inter-layer region are accessible to chiral analytes, resulting in a tenfold enhanced sensitivity in a chiral sensing proof-of-concept experiment. In situ restacking and local mechanical compression enables full control over the entire set of circular dichroism characteristics, namely sign, magnitude and spectral position. Strain-induced reconfiguration opens up an intriguing route towards actively controlled pixel arrays using local deformation, which fosters continuous polarization engineering and multi-channel detection. Stacked elastomeric arrays containing plasmonic nanoparticles show efficient chiral responses that can be fully controlled by mechanical compression and stack rotation. These simple layered materials may be useful modulators for photonic applications.

Aim To understand how functional traits and evolutionary history shape the geographic distribution of plant life on Earth, we need to integrate high‐quality and global‐scale distribution data with functional and phylogenetic information. Large‐scale distribution data for plants are, however, often restricted to either certain taxonomic groups or geographic regions. Range maps only exist for a small subset of all plant species and digitally available point‐occurrence information is biased both geographically and taxonomically. Floras and checklists represent an alternative, yet rarely used potential source of information. They contain highly curated information about the species composition of a clearly defined area, and together virtually cover the entire global land surface. Here, we report on our recent efforts to mobilize this information for macroecological and biogeographical analyses in the GIFT database, the Global Inventory of Floras and Traits. Location Global. Taxon Land plants (Embryophyta). Methods GIFT integrates plant distributions from regional Floras and checklists with functional traits, phylogenetic information, and region‐level geographic, environmental and socio‐economic data. It contains information about the floristic status (native, endemic, alien and naturalized) and takes advantage of the wealth of trait information in the regional Floras, complemented by data from global trait databases. Results GIFT 1.0 holds species lists for 2,893 regions across the whole globe including ~315,000 taxonomically standardized species names (i.e. c. 80% of all known land plant species) and ~3 million species‐by‐region occurrences. Based on a hierarchical and taxonomical derivation scheme, GIFT contains information for 83 functional traits and more than 2.3 million trait‐by‐species combinations and achieves unprecedented coverage in categorical traits such as woodiness (~233,000 spp.) or growth form (~213,000 spp.). Main conclusions Here, we present the structure, content and automated workflows of GIFT and a corresponding web‐interface (http://gift.uni-goettingen.de) as proof of concept for the feasibility and potential of mobilizing aggregated biodiversity data for global macroecological and biogeographical research.