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Povzetek: Background Allele-specific expression analysis can reveal cis-regulatory differences (e.g., promoter variants, epigenetic changes) that cause imbalanced gene expression between haplotypes. Haplotype-resolved reference genomes and long-read RNA sequencing enable allele-specific expression analysis at gene and isoform-levels. However, existing tools are largely restricted to short-read RNA sequencing data and diploid organisms. Results We developed LongPolyASE, an end-to-end computational framework for allele-specific gene and isoform expression analysis in diploid and polyploid organisms using long-read RNA sequencing, consisting of three components: Syntelogfinder, for identifying syntenic gene relationships and annotation inconsistencies; longrnaseq, for novel isoform discovery and haplotype-level quantification; and PolyASE, for statistical testing and visualization of allelic imbalance and isoform usage. We applied LongPolyASE to diploid rice, autotetraploid potato, allotetraploid rapeseed, and allooctoploid strawberry using Oxford Nanopore and PacBio long-read RNA-seq. The framework enabled identification of cis-regulatory variation, tissue-specific trans-regulatory effects, differential isoform usage, and haplotype-specific splicing differences. In addition, it facilitated the discovery of novel transcripts and genes with potential functional relevance in plant development. Conclusions LongPolyASE addresses a key methodological gap by enabling allele-specific expression analysis in polyploid organisms using long-read RNA sequencing. By combining haplotype-aware quantification with isoform-level resolution in a reproducible workflow, the framework provides a practical tool for plant researchers working with complex genomes. Its application to crop species highlights its potential to support the identification of regulatory variation and candidate targets for plant breeding.
Ključne besede: allele-specific expression analysis, polyploids, long-read RNA-seq, isoform expression, gene expression
Objavljeno v DiRROS: 03.08.2026; Ogledov: 242; Prenosov: 147
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Ključne besede: potato virus Y, coat protein, viral movement, point mutations, Solanum tuberosum
Objavljeno v DiRROS: 31.03.2026; Ogledov: 458; Prenosov: 508
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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
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Objavljeno v DiRROS: 26.11.2025; Ogledov: 865; Prenosov: 443
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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: 1336; Prenosov: 611
Celotno besedilo (1,82 MB)
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