1. Predstavitev programskih orodij Python in RMaja Zagorščak, Carissa Bleker, Jan Zrimec, Marko Petek, Anže Županič, 2024, drugo učno gradivo Ključne besede: podatki, ravnanje s podatki, ravnanje z raziskovalnimi podatki, raziskovalni podatki, odprta znanost, programska orodja, Python, R
Objavljeno v DiRROS: 26.05.2025; Ogledov: 211; Prenosov: 109
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3. Protein complexes from edible mushrooms as a sustainable potato protection against coleopteran pestsKarmen Pogačar, Maja Grundner, Primož Žigon, Anna Coll Rius, Anastasija Panevska, Tjaša Lukan, Marko Petek, Jaka Razinger, Kristina Gruden, Kristina Sepčić, 2024, izvirni znanstveni članek Ključne besede: biopesticides, Leptinotarsa decemlineata, Solanum tuberosum, insect stress response, larval toxicity, transgenic crop
Objavljeno v DiRROS: 14.05.2025; Ogledov: 155; Prenosov: 75
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4. Combining short- and long-read transcriptomes for targeted enzyme discoveryMojca Juteršek, Marko Petek, Špela Baebler, 2025, samostojni znanstveni sestavek ali poglavje v monografski publikaciji Povzetek: The discovery of genes that code for a specific enzymatic activity is important in various fields of life science and provides valuable biotechnological tools. Many genes that contribute to the production of secondary metabolites and specialized metabolic pathways are still not identified. Due to the great diversity of metabolic functions found in nature and their rapid evolutionary adaptation, we need precise but high-throughput approaches for a targeted search based on minimal prior knowledge. In this chapter, we describe a transcriptomics pipeline that was used to search for candidate genes coding for a specific enzymatic activity in a nonmodel species. We generated and combined short- and long-read transcriptomic data to obtain reliable full-length transcript sequences along with information on allelic variation, isoform expression, and condition-specific expression. Based on protein domain annotations of coding sequences and transcriptomic data, we selected candidate genes for activity assays. We provide detailed instructions for analysis and quality control steps in our pipeline that can be applied to other biological questions.
Ključne besede: genes, enzymatic activity, transcriptomics, metabolic pathways, allelic variation, isoform expression, biotechnological tools
Objavljeno v DiRROS: 14.04.2025; Ogledov: 287; Prenosov: 116
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5. Ethylene signaling is essential for mycorrhiza-induced resistance against chewing herbivores in tomatoJavier Lidoy, Javier Rivero, Živa Ramšak, Marko Petek, Maja Križnik, Victor Flors, Juan A Lopez-Raez, Ainhoa Martinez-Medina, Kristina Gruden, Maria J Pozo, 2025, izvirni znanstveni članek Povzetek: Arbuscular mycorrhizal (AM) symbiosis can prime plant defenses, leading to mycorrhiza-induced resistance (MIR) against different attackers, including insect herbivores. Still, our knowledge of the complex molecular regulation leading to MIR is very limited. Here, we showed that the AM fungus Funneliformis mosseae protects tomato plants against two different chewing herbivores, Spodoptera exigua and Manduca sexta. We explored the underlying molecular mechanism through genome-wide transcriptional profiling, bioinformatics network analyses, and functional bioassays. Herbivore-triggered jasmonate (JA)-regulated defenses were primed in leaves of mycorrhizal plants. Likewise, ethylene (ET) biosynthesis and signaling were also higher in leaves of mycorrhizal plants both before and after herbivory. We hypothesized that fine-tuned ET signaling is required for the primed defense response leading to MIR. ET is a complex regulator of plant responses to stress and is generally considered a negative regulator of plant defenses against herbivory. However, ET-deficient or insensitive lines did not show AM-primed JA biosynthesis or defense response, and were unable to develop MIR against any of the herbivores. Thus, we demonstrate that hormone crosstalk is central to the priming of plant immunity by beneficial microbes, with ET fine-tuning being essential for the primed JA biosynthesis and boosted defenses leading to MIR in tomato.
Ključne besede: chewing herbivores, defense priming, ethylene, hormonal crosstalk, jasmonate, mycorrhiza-induced resistance (MIR)
Objavljeno v DiRROS: 10.04.2025; Ogledov: 311; Prenosov: 204
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6. Orodja za delo z delotokiMarko Vidak, Bojan Kverh, Polonca Ferk, Branimir Leskošek, Maja Zagorščak, Nadja Francesca Nolte, Carissa Bleker, Marko Petek, Anže Županič, 2024, druge monografije in druga zaključena dela Ključne besede: odprti podatki, odprta znanost, delo z delotoki, projekt Spoznaj, okolje Galaxy, raziskovalni podatki, uporabljanje podatkov
Objavljeno v DiRROS: 12.03.2025; Ogledov: 358; Prenosov: 125
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7. Protein complexes from edible mushrooms as a sustainable potato protection against coleopteran pestsKarmen Pogačar, Maja Grundner, Primož Žigon, Anna Coll Rius, Anastasija Panevska, Tjaša Lukan, Marko Petek, Jaka Razinger, Kristina Gruden, Kristina Sepčić, 2024, izvirni znanstveni članek Ključne besede: biopesticides, Leptinotarsa decemlineata, Solanum tuberosum, insect stress response, larval toxicity, transgenic crop
Objavljeno v DiRROS: 30.01.2025; Ogledov: 301; Prenosov: 206
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8. Haplotype-resolved genome assembly of the tetraploid potato cultivar DésiréeTim Godec, Sebastian Beier, Natalia Yaneth Rodriguez-Granados, Rashmi Sasidharan, Lamis Abdelhakim, Markus Teige, Björn Usadel, Kristina Gruden, Marko Petek, 2025, drugi sestavni deli 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: 368; Prenosov: 200
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9. Editorial : Mechanisms of plant host resistance against virusesRégis L. Corrêa, Marko Petek, Maite F. S. Vaslin, 2024, drugi znanstveni članki Ključne besede: plants, pathogens, plant viruses, resistance, biotechnological tools, CRISPR/Cas9, agriculture, biotechnology
Objavljeno v DiRROS: 05.11.2024; Ogledov: 720; Prenosov: 229
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10. Milestone M27 : user friendly data management and analysis environment for plant systems biology established and novel/improved multiomics data visualisation tool availableLuka Ausec, Barbara Jenko Bizjan, Janez Kokošar, Amrita Roy Choudhury, Miha Štajdohar, Kristina Gruden, Maja Križnik, Marko Petek, Živa Ramšak, 2018, končno poročilo o rezultatih raziskav Povzetek: We present the technical report regarding the implementation of the Genialis Platform at the National Institute of Biology (NIB) within the project Hyp (J4-7636).
Objavljeno v DiRROS: 05.09.2024; Ogledov: 547; Prenosov: 350
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