Department of Plant Developmental Genetics
Head: Roman Hobza
Genome Dynamics
We focus on understanding the dynamics of plant genomes in the context of the reproductive strategies of individual species. Our goal is to uncover the role of transposable elements in the evolution and regulation of gene expression, replication, and the structure of individual chromosomes. In our research, we employ single-cell (chromosome) genomics and transcriptomics approaches, combined with sophisticated bioinformatic tools.
Bioinformatics
For sophisticated analyses of genome structure and function, we frequently develop and test our own software. To decipher the complex genetic and epigenetic regulatory networks underlying plant developmental processes, we establish appropriate pipelines that combine tools such as GWAS, Gene Ontology enrichment analysis, LinkYX for genetic linkage analysis, TE-greedy-nester for transposable element identification, HiC-TE: a pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization, and LTR_BERT: a classification of long terminal repeat sequences in plant LTR-retrotransposons using explainable machine learning. Additionally, we apply morphometric analysis to quantify seed size, shape and structure using modern geometric tools in combination with Elliptic Fourier transformation.
Floral Development
We are searching for key genes that influence the flowering process across model and non-model species, including crops. We employ cutting-edge molecular biology tools such as CRISPR/Cas9 genome editing, Transcription Activator-Like Effector Nucleases (TALENs), and RNAi silencing for functional characterization of genes and regulatory elements. These molecular tools enable precise manipulation of the plant genome, facilitating the study of gene function and regulatory mechanisms governing plant development and reproduction.
Sex Chromosome Biology
Our research aims to uncover the evolutionary mechanisms driving sex chromosome evolution, Y degeneration, and the evolution of dosage compensation. We employ a combination of already listed genomic, bioinformatic, and cytogenetic techniques (high-throughput imaging with AI assisted image segmentation, oligo-painting, super-resolution techniques and electron microscopy) to elucidate the genetic and epigenetic factors governing sex chromosome differentiation and regulation, including the role of chromosomal rearrangements in the sex chromosome formation, and impact of recombination suppression on epigenomic landscape of XY (ZW) chromosomes.
Epigenetics and Chromatin Structure
Epigenetic processes are essential for understanding the principles of development. Additionally, they play a key role in adaptation processes. We investigate the role of epigenetic modifications and chromatin organization in regulating gene expression and plant development, in the context of sex chromosome evolution. We use Chromatin Immunoprecipitation Sequencing (ChIP-seq), Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq), Cleavage Under Targets and Release Using Nuclease (CUTandRUN) methodology and various cytological methods.
Research model plants
Our primary research focuses on dioecious species and hermaphrodite plants within the following genera: Silene, Rumex and Humulus.
Laboratory of Applied Biotechnology in Agriculture
Our laboratory aims to leverage all the aforementioned tools in addressing issues related to the impacts of global climate change on agriculture. We collaborate particularly with European breeders to integrate molecular methods and genome editing into the breeding process. Furthermore, we aim to monitor soil microbiomes and investigate causal factors influencing plant development and their resilience to biotic and abiotic stresses. We are also aiming to adjust the characteristics of microorganisms, including algae, for enhanced biotechnological applications.
Laboratory of Applied Biotechnology in Agriculture was established as part of the Food for the Future AV21 Strategy program in 2021.