Maja Zagorscak

• National Institute of Biology

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 prof...

Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the...

Plants respond to stress by redistributing resources from growth- to defence-related processes, often resulting in decreased yields. Understanding the molecular mechanisms behind these growth-defence trade-offs can enhance breeding strategies to help us design crop varieties with improved stress tolerance, yields and quality. To enable the investig...

Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non‐model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ra...

Potato, the most important non-cereal crop, is highly water and space efficient but susceptible to abiotic stress such as heat, drought, or flooding. Climate change is severely increasing the likelihood of such stresses to occur individually, sequentially, or simultaneously. However, the understanding of acclimation to abiotic stress in crops in ge...

Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant re-analysis, and leads to missing or wrongly anno...

Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge networ...

Background Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies...

Potato (Solanum tuberosum) is the most popular tuber crop and model organism. Though its gene models are frequently updated, they are not unified, leading to missing or wrongly annotated genes. Here, we thus unify the recent potato double monoploid v4 and v6 gene models by automatic merging. We established an Apollo web server that enables access t...

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CK...

The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including ‘Candidiatus Phytoplasma solani’ are unknown. Six putative pathogenicity factors/effectors from six different strains of ‘Ca. P. solani’ were selected by...

Background: Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologie...

We developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. pISA-tree was initiated by end-user requirements thus its strong points are practicality and low maintenance cost. It enables on-the-fly creation of enriched directory tree structure (projec...

Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol...

We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on-the-fly creation of enriched directory tree structure (project/Investigation/Study/Assay) via a series of sequential batch files in a standardised manner based on the ISA...

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 reg...

We have witnessed a rapid advancement in high-throughput genome sequencing and the maturation of long-read technologies. However, an accurate assembly of polyploid potato genomes still remains challenging. Sequencing the double-monoploid genome of Solanum tuberosum Group Phureja (Xu et al., Nature 475:189–195, 2011) has enabled functional studies o...

Background Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which are of them being plant elicitor peptides (Peps). Exogenous application of Peps activates defense mechanisms an...

see all Supplementary Information at https://fairdomhub.org/assays/1261 under the project https://fairdomhub.org/projects/161

While activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to restriction of pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny‐1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the bi...

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted inve...

While activation of resistance (R) proteins has been intensively studied, the mechanisms acting downstream of R protein activation remain elusive. We studied effector-triggered immunity (ETI) conditioned by the potato Ny-1 gene against potato virus Y. Transcriptomic, ultrastructural and biochemical analyses of four consecutive tissue sections in an...

Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted inve...

The “Advanced Big Data Training School for Life Sciences” took place during September 3-7, 2018, organized by the Data Management Group (DAMA-UPC) at the Technical University of Catalonia (UPC) in Barcelona, Spain. It is the follow-up training school of the first “Big Data Training School for Life Sciences”, held in Uppsala, Sweden, in September 20...

Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available...

Background Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental data are superimposed on a pri...

Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These methods often depend on the wealth of information already collected. The explosion in the number of newly available...

On 6th and 7th February 2018, a Think Tank took place in Ljubljana, Slovenia. It was a follow-up of the “Big Data Training School for Life Sciences” held in Uppsala, Sweden, in September 2017. The focus was on identifying topics of interest and optimising the programme for a forthcoming “Advanced” Big Data Training School for Life Science, that we...

Hypersensitive response (HR)-conferred resistance to viral infection restricts the virus spread and is accompanied by the induction of cell death, manifested as the formation of necrotic lesions. While it is known that salicylic acid is the key component in the orchestration of the events restricting viral spread in HR, the exact function of the ce...

Dynamics of lesion expansion in cv. Rywal after PVY N605-GF Pinoculation. Lesions expansion was followed by DinoLite digital microscope in 13 independent experiments. Black arrows indicate some of the lesions which continuously expanded even in later dpi, while red arrows indicate some of the lesions which became fully developed already in early ti...

Dynamics of lesion expansion in Rywal after PVY N605-GFP infection.

Dynamics of lesion expansion in NahG-Rywal after PVY N605-GFP inoculation. Lesions expansion was followed by DinoLite digital microscope in 5 independent experiments. We observed unlimited expansion of all analyzed lesions.

(A) Number of lesions with the PVY N605-GFP accumulation detected outside the cell death zone after inoculation. Results from seven independent experiments (Exp 1–7) are presented for cv. Rywal and NahG-Rywal. At each time point (3–12 dpi) one or two plants (A,B) were analyzed (one leaf per plant). Number of positive lesions (number of lesions with...

Dynamics of lesion expansion in NahG-Rywal after PVY N605-GFP infection.

Number of lesions developed on potato leaves after inoculation with PVY N605-GFP. Lesions were counted in 16 cv. Rywal and 11 NahG-Rywal plants on all three inoculated leaves from 3 to 7 dpi and on 11 dpi to study the dynamics of lesions formation. (A) Numbers of lesions observed on each plant leaf at each time point is shown. X: detached leaf for...

The probability that the observed lesion was formed until the particular day post inoculation. The probability was calculated after PVY N605-GFP inoculation of cv. Rywal (A) and NahG-Rywal (B) plants by nonlinear regression model with logistic function.

Relative PVY RNA abundance in the systemic leaves in Rywal and NahG-Rywal plants after PVY inoculation. Relative PVY RNA abundance was determined in upper non-inoculated leaves 4 weeks after inoculation with PVY N605-GFP. Results were obtained from two independent experiments. Relative abundance of PVY RNA was followed using quantitative PCR. RNA w...

This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel...

Most potato cultivars are highly heterozygous tetraploids with high genetic variability while being susceptible to pathogens, pests and inbreeding depression. To bypass polyploidy related sequencing problems, Potato Genome Sequencing Consortium (PGSC, 2011) sequenced a double monoploid derived from S. tuberosum group Phureja.