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Povzetek: UniTato: a web server for evidence and community based Unification of poTato gene models
Ključne besede: bioinformatics analysis, plant genome annotation, gene model annotations, Phureja group, GFF files, poTato genome model, UniTato
Objavljeno v DiRROS: 08.05.2026; Ogledov: 398; Prenosov: 460
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Povzetek: 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.
Ključne besede: plant pan-genome, white paper, standards, quality control
Objavljeno v DiRROS: 24.02.2026; Ogledov: 614; Prenosov: 326
Celotno besedilo (1,20 MB)
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Povzetek: We investigated the spatial dynamics of potato (Solanum tuberosum) responses to herbivory and mechanical wounding. We first followed the spatiotemporal response of jasmonic acid (JA) signaling, known to be involved in the response. We generated two potato sensor lines: a JAZ degradation sensor and a downstream multicystatin (MC) transcriptional reporter. Both sensors revealed concentric, locally restricted responses on wounded leaves. Notably, JAdependent gene expression was absent in cells immediately adjacent to the wound, whereas JAZ degradation spread continuously outward from the wound site. This pattern occurred after both herbivore attack and mechanical injury by the needle. To probe the mechanism, a salicylic acid (SA) reporter showed SA accumulation near the wound. Introducing the MC reporter into SA-depleted NahG plants produced a uniform spread of MC expression, confirming that SA attenuates the JA response in proximal cells. Together, these results show that a locally distinct, spatiotemporal SA–JA crosstalk shapes wound responses in potato, extending principles known from pathogen–plant interactions to herbivory and mechanical damage.
Ključne besede: Colorado potato beetle, herbivore, hormonal crosstalk, jasmonic acid, potato, salicylic acid, wounding
Objavljeno v DiRROS: 28.01.2026; Ogledov: 650; Prenosov: 696
Celotno besedilo (4,03 MB)
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Povzetek: Understanding the molecular mechanisms behind plant response to stress can enhancebreeding strategies and help us design crop varieties with improved stress tolerance,yield, and quality. To investigate resource redistribution from growth- to defense-relatedprocesses in an essential tuber crop, potato, here we generate a large-scale compartmen-talized genome-scale metabolic model (GEM), potato-GEM. Apart from a large-scalereconstruction of primary metabolism, the model includes the full known potato sec-ondary metabolism, spanning over 566 reactions that facilitate the biosynthesis of 182distinct potato secondary metabolites. Constraint-based modeling identifies that theactivation of the largest amount of secondary (defense) pathways occurs at a decreaseof the relative growth rate of potato leaf, due to the costs incurred by defense. We thenobtain transcriptomics data from experiments exposing potato leaves to two bioticstress scenarios, a herbivore and a viral pathogen, and apply them as constraints toproduce condition-specific models. We show that these models recapitulate experimen-tally observed decreases in relative growth rates under treatment as well as changes inmetabolite levels between treatments, enabling us to pinpoint the metabolic rewiringunderlying growth–defense trade-offs. Potato- GEM thus presents a useful resource tostudy and broaden our understanding of potato and general plant defense responsesunder stress conditions.
Ključne besede: systems biology, constraint-based metabolic modeling, growth-defence trade-offs, secondary metabolism
Objavljeno v DiRROS: 24.09.2025; Ogledov: 1335; Prenosov: 611
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Povzetek: Small RNAs (sRNAs) are short noncoding RNAs involved in the regulation of a wide range of biological processes in plants. Advances in high-throughput sequencing and development of new computational tools had facilitated the discovery of different classes of sRNAs, their quantification, and elucidation of their functional role in gene expression regulation by target transcript predictions. The workflow presented here allows identification of different sRNA species: known and novel potato miRNAs, and their sequence variants (isomiRs), as well as identification of phased small interfering RNAs (phasiRNAs). Moreover, it includes steps for differential expression analysis to search for regulated sRNAs across different tested biological conditions. In addition, it describes two different methods for predicting sRNA targets, in silico prediction, and degradome sequencing data analysis. All steps of the workflow are written in a clear and user-friendly way; thus they can be followed also by the users with minimal bioinformatics knowledge. We also included several in-house scripts together with valuable notes to facilitate data (pre)processing steps and to reduce the analysis time.
Objavljeno v DiRROS: 06.08.2025; Ogledov: 905; Prenosov: 552
Celotno besedilo (1,17 MB)
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