The most important achievements

Institute of Plant Genetics PAS in 2025

Regulation of Gene Expression Team

Using ChIP-seq and global transcriptome analysis of Solanum tuberosum cv. Desirée plants with overexpression and silenced expression of StBBX20 gene, we identified target genes for StBBX20 protein (formerly StBBX24) specific to the light-dark cycle and involved in the flowering and flower development process and the induction of tuberization in the cultivated potato species, such as CONSTANS interacting protein 2a, StHY5, StRAPTOR1B, StSPL, StMADS47, StMADS153, StSOC1 and StSUP, StBEL5, StPOTH1, StGA2ox1 and StSP6A.

Grądzka, K; Biegańska, M; Koczyk, G; Młodzińska, A; Pawłowicz, I; Kiełbowicz-Matuk, A (2025) CHIP-seq and transcriptomics reveal a new role of circadian-regulated StBBX24 protein in potato reproduction. BMC Plant Biology 25: 1702.

Plant Physiology Team

The genome sequence and annotation of allotetraploid species Festuca galucescens were recognized using next-generation sequencing (PacBio and Illumina) and RNAseq analysis. Furthermore, repetitive sequences present in the genome were analyzed. This is the first genome of a grass in the Festuca genus to be described.

Pawłowicz, I; Kopeć, P; Kosmala, A (2025) The draft genome assembly and annotation of allotetraploid Festuca glaucescens. BMC Plant Biology 25: 1590.

Biometry and Bioinformatics Team

A methodology for identifying the genes of secondary metabolite biosynthesis through phylogenetic placement was developed and validated as an open-source tool for identifying the genes of polyketide synthases (HR-PKSs) involved in benzenediol lactone (BDL) biosynthesis in fungi. The tool enables low-cost phylogenetic classification of incomplete sequences (amplicons or reads) for screening sequence data for diverse gene families.

Kawaliło, M; Lalak-Kańczugowska, J; Dutkiewicz, Z; Urbaniak, M; Popiel, D; Czyż, K; Koczyk, G (2025) Rational deployment of molecular markers for the benzenediol lactones and related compounds biosynthesis in filamentous fungi. PeerJ 13: e20472.

Cereal Phenomics Team

For the first time, the expression of melatonin biosynthesis genes in barley roots under drought conditions was characterized, indicating key roles for TDC1 and TDC3 genes. It was shown that the induction of TDC activity in response to drought and melatonin application occurs only in genotypes with proper brassinosteroid signaling, which, when disrupted, limits melatonin biosynthesis. This phenomenon confirms the fact that the interaction of melatonin and brassinosteroids is essential for the plant's full response to water deficit.

Plant Biotechnology Team

The response of selected Miscanthus species and genotypes to abiotic stresses was comprehensively characterized: (i) chilling stress and (ii) soil arsenic contamination. The obtained results enabled the identification of diverse stress tolerance mechanisms in these grasses and indicated their adaptive and utility potential.

Sobańska, K; Głowacka, K; Krajewski, P; Wojtkowiak, E; Nuc, M; Basińska-Barczak, A; Czyż KB; Waligórski, P; Kruszka, D; Gabała, E; Grzywaczyk, A; Zborowska, M; Drożdżyńska, A; Mokrzycka, M; Koczyk, G; Cerazy-Waliszewska, J; Milewska-Hendel, A; Betekhtin, A; Pniewski T (2025) From Stress to Recovery: Divergent Chilling Responses in Contrasting Miscanthus sinensis Genotypes. GCB Bioenergy 17: e70087.

Cerazy-Waliszewska, J; Wojciechowska, Z; Bialas, W; Mleczek, M; Niedzielski, P; Proch, J; Pniewski, T (2025) Effect of arsenic speciation on growth, physiology, and bioethanol yield in two Miscanthus x giganteus genotypes. Journal of Environmental Management 394: 127343.

Pathogen Genetics and Plant Resistance Team

The G476S substitution in CYP51 gene has been shown to lead to a reduced susceptibility of Plenodomus biglobosus to triazole fungicides. Duplications in the promoter of CYP5 gene sequence were also found in 8% of isolates, but no changes involving transposons transferred to the promoter of CYP51were observed, which is the mechanism of loss of triazole susceptibility in the related species P. lingam. We demonstrate that both species have evolved different mechanisms allowing them to colonize oilseed rape plants treated with triazole fungicides.

King, KM; González-Rodriguez, LM; Kaczmarek, J; Jedryczka, M; West, JS (2025) Decreased DMI sensitivity of Plenodomus biglobosus (phoma of oilseed rape) associated with CYP51 substitution G476S. Pest Management Science. DOI: 10.1002/ps.8926

Plant - Pathogen Interaction Team

Mulberry leaf extract has been shown to effectively inhibit the growth and production of fumonisins, as well as to inhibit the expression of FUM genes in Fusarium proliferatum.

Plant Microbiomics Team

For the first time, the diversity of endophytic fungi associated with the medicinal plant Calicotome spinosa was described and it was shown that it may constitute a reservoir for diverse and potentially stress-resistant fungal symbionts, known for their ecological plasticity and functional diversity. The presence if these fungi in plant tissues may contribute to the strengthening of plant condition and functioning in the Mediterranean environment.

Zareb, A; Banachewicz, P; Havrysh, P; Błaszczyk, L; Hammad, T; Meftah, C; Salamon, S (2025) Endophytic fungal communities of Calicotome spinosa—an important medicinal plant of Tizi-Ouzou (Algeria). Journal of Applied Genetics 66: 763-769.

Legume Genomics Team

A comparative overview of the genetic and regulatory determinants of low alkaloid content in narrow-leafed lupin was obtained by comparing two distinct genetic backgrounds (iucundus and Bryansk lines). Candidate genes for unrecognized steps of biosynthesis and expression changes associated with iucundus-independent regulation, were found. A binding motif for the transcription factor RAP2-7 was identified and the R196S substitution was associated with impaired DNA binding and low alkaloid levels.

Czepiel, K; Burdzińska, A; Susek, K; Kiełbowicz- Matuk, A; Koczyk, G; Kroc, M Multi-omics insights into quinolizidine alkaloid biosynthetic architecture in narrow-leafed lupin genotypes with contrasting alkaloid regulation. BioRxiv, DOI: 10.64898/2026.01.08.698079.

Gene Structure and Function Team

In a pool of 173 Spanish lupin (Lupinus hispanicus) genotypes, using the method of genome association mapping, a significant association with flowering date and vernalization response was identified for a number of DArT-seq markers located in genomic regions containing genes involved in flowering regulatory pathways. Based on these results, parental components were selected to create mapping populations, which will be used in further studies.

Bielski, W; Surma, A; Belter, J; Kozak, B; Ksiazkiewicz, M; Rychel-Bielska, S (2025) Molecular dissection of the genetic architecture of phenology underlying Lupinus hispanicus early flowering and adaptation to winter- or spring sowing. Scientific Reports 15: 15324. DOI: 1038/s41598-025-00096-1.

Integrative Plant Biology Team

A spatial and temporal course of induction of PEAR family genes during infection by Plasmodiophora brassicae, and the effect of mutations in these genes on gall development in Arabidopsis thaliana, were described.

Singh, D; Blicharz, S; Roszak, P; Helariutta, Y; Malinowski, R (2025) PHLOEM EARLY DOF genes are induced within clubroot galls as a consequence of cambial stimulation and vascular reprogramming during Plasmodiophora brassicae infection in Arabidopsis thaliana. Journal of Experimental Botany 76: 45214537.

Plant Biology and Nanotechnology Team

Our research achievement focused on elucidating the complex molecular interactions between Hypericum perforatum and Agrobacterium species. We performed a dual-omics comparison to reveal how Agrobacterium tumefaciens and Agrobacterium rhizogenes differentially modulate gene expression and metabolism in H. perforatum (BMC Genomics, 2025). This was complemented by a study detailing the specific proteomic remodeling and physiological adaptations induced by A. tumefaciens (Plant Stress, 2025). Additionally, we achieved transgenic validation of a novel H. perforatum promoter that is strongly and specifically inducible by A. tumefaciens, providing a new genetic tool for precise, pathogen-responsive gene regulation (Scientific Reports, 2025).

Selvakesavan’ RK; Nuc, M; Pradeep, M; Krajewski, P; Gregory, F (2025) Dual omics comparison: how Agrobacterium tumefaciens and Agrobacterium rhizogenes modulate gene expression and metabolism in Hypericum perforatum L. BMC Genomics 26 (1): 958.

Shakya, P; Selvakesavan, RK; Perlikowski, D; Antonydhason, V; Kiirika, L; Gregory, F (2025) Agrobacterium tumefaciens-induced proteomic remodelling and physiological adaptations in Hypericum perforatum L. Plant Stress 18: 100986.

Sinha, RK; Shakya, P; Selvakesavan, RK; Gregory, F (2025) Transgenic validation of a promoter strongly inducible by Agrobacterium tumefaciens. Scientific Reports 16: 485.

Plant Nanotechnology Team

Published circular valorization of Hypericum perforatum biomass into CuO-lignin and CuO-cellulose bionanocomposites for mitigating copper nanotoxicity in plants (NANOPLANT). Published the novel strategy for packaging of HPR against biotic stress using DNA and ionic liquid-based bioinspired solvent (SONATA 17).

Saxena, M; Muthukrishnan, L; Pradeep, M; Selvakesavan, RK; Franklin, G; Mondal, D (2025) Circular valorization of Hypericum perforatum biomass into CuO-lignin and CuO-cellulose bionanocomposites for mitigating copper nanotoxicity in plants. International Journal of Biological Macromolecules 321: 146474.

Dhiman, D; Sethi, A; Sinha, R; Biswas, S; Franklin, G; Mondal, D (2025) Bioinspired design of DNA in aqueous ionic liquid media for sustainable packaging of horseradish peroxidase under biotic stress. Chemical Communications 61 (8): 1613-1616.