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Povzetek: Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.
Ključne besede: potato, Solanum tuberosum, abiotic stress responses, heat, drought, waterlogging, multi-omics, integrative omics, adaptomics, panomics
Objavljeno v DiRROS: 14.04.2025; Ogledov: 161; Prenosov: 127
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Povzetek: The ELIXIR Plant Sciences Community is an interdisciplinary group of researchers with diverse backgrounds from computer science to different fields of plant biology. We answer the needs of both bioinformaticians and plant biologists. The Community objective is to develop services supporting the integration and linking of phenotypic, genotypic, omics (e.g. expression, metabolomics, etc.), environmental, and bibliographic data. The underlying scientific use cases encompass fundamental and applied plant sciences, including genetics, system biology and omics approaches, within the broader context of climate change, agroecology, food security, and sustainable agriculture. To meet the current challenges in agriculture, the ELIXIR Community promotes tools, databases, standards, and best practices for plant research while developing joint initiatives such as international projects and events in collaboration with European infrastructures (EMPHASIS, AnaEE-ERIC, Euro-Bioimaging, METROFOOD-RI). The ELIXIR Community also supports the establishment of links to structuring national projects and initiatives such as NFDI in Germany, or the french Agroecology and ICT program. Despite ongoing efforts, challenges remain, such as the continued scattering of plant molecular and cellular data, which hampers efficient data integration and reuse. Additionally, progressing toward a comprehensive agriculture data space is essential to address the interdisciplinary challenges that modern agriculture faces. Strengthening engagement with related research communities, such as those working on plant pathogens, is also a priority to ensure a holistic approach to plant science and agricultural research. Finally the Plant Sciences Community links with other ELIXIR Communities and Focus Groups, in particular to contribute to the objectives and priority of the Biodiversity, Food Security and Pathogens and of the Cellular and Molecular Research scientific priority areas.
Ključne besede: system biology, genotyping, plant
Objavljeno v DiRROS: 04.04.2025; Ogledov: 205; Prenosov: 54
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Povzetek: Background: Different immunotherapy approaches for the treatment of cancer andautoimmune diseases are being developed and tested in clinical studies worldwide. Their resulting complex experimental data should be properly evaluated, therefore reliable normal healthy control baseline values are indispensable. Methodology/Principal Findings: To assess intra- and inter-individual variability of various biomarkers, peripheral blood of 16 age and gender equilibrated healthy volunteers was sampled on 3 different days within a period of one month. Complex ććcrossomicsćć analyses of plasma metabolite profiles, antibody concentrations and lymphocyte subset counts as well as whole genome expression profiling in CD4+T and NK cells were performed. Some of the observed age, gender and BMI dependences are in agreement with the existing knowledge, like negative correlation between sex hormone levels and age or BMI related increase in lipids and soluble sugars. Thus we can assume that the distribution of all 39.743 analysed markers is well representing the normal Caucasoid population. All lymphocyte subsets, 20% of metabolites and less than 10% of genes, were identified as highly variable in our dataset. Conclusions/Significance: Our study shows that the intra-individual variability was at least two-fold lower compared to the inter-individual one at all investigated levels, showing the importance of personalised medicine approach from yet another perspective.
Objavljeno v DiRROS: 04.03.2025; Ogledov: 166; Prenosov: 140
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Povzetek: Glucanases are enzymes regulating the size exclusion limit and permeability of plasmodesmata and play a role in biotic stress. In plant genomes, they are encoded as relatively large gene families divided into four classes. Most studies of plant virus interactions have focused on glucanases from classes I and II. In our study, we have evaluated the role of the β-1,3-glucanase class III (Glu-III) gene in the potato–potato virus YNTN (PVYNTN) interaction and implemented the findings to plant biotechnology application. Potato cultivars Désirée and Santé, which are tolerant and extremely resistant to PVYNTN, respectively, were stably transformed with Agrobacterium tumefaciens harbouring constructs for Glu-III overexpression. Localization of Glu-III protein in patches within the cell wall was determined by tagging the Glu-III protein with green fluorescent protein. Transgenic and non-transgenic plants were challenged with PVYNTN and its multiplication and spreading was followed. Differences in viral spread were observed between transgenic lines overexpressing Glu-III and non-transgenic lines, with stronger and faster viral spread in transgenic Désirée, and some multiplication in transgenic Santé. In addition, the ability of Glu-III to improve in planta protein production after agroinfiltration was tested. The results have shown that Glu-III overexpression enables faster spreading of vectors between cells and better protein production, which could be beneficial in improving in planta protein production system using viral vectors.
Ključne besede: plant biotechnology, plant-virus interaction, potato virus Y, agroinfiltration, beta-1, 3-glucanase
Objavljeno v DiRROS: 04.03.2025; Ogledov: 268; Prenosov: 497
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Povzetek: Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser (https://desiree.nib.si), providing a valuable resource for the potato research community.
Ključne besede: cultivar Désirée, potato, functional genomics, genome assembly, annotation pipeline, DNA methylation, epigenetics
Objavljeno v DiRROS: 28.01.2025; Ogledov: 254; Prenosov: 132
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