1. Laboratory of Molecular Systematics In this laboratory we generate data addressing scientific questions of taxonomy, phylogeny, phylogeography and related evolutionary processes across different groups of vascular and non-vascular plants. Methods applied are focused on the study of differences and changes on the DNA level among organisms using several methods such as AFLP (Amplified Fragment Length Polymorphism), SSRs (microsatellites – simple repetitions) or sequencing of selected loci. Most of the currently used molecular methods are based on variations of the PCR (Polymerase Chain Reaction) and the analyses of the relevant products. The laboratory is also equipped for DNA extraction from plant material dried in silica gel or from herbarium specimens. In case when direct sequencing of specific loci is problematic, we use methods such as SSCP (Single-Strand Conformation Polymorphism) or cloning of PCR products into the bacterial cells, separating different alleles from diploid and especially from polyploid individuals. Currently we implement also new methods based on the NGS (Next Generation Sequencing), such as a Hyb-Seq and RAD-Seq. Here we are sequencing only selected loci and not the whole genome, which decreases price per sample and gives the opportunity to sequence more individuals. The laboratory of molecular systematics possess all necessary equipment for standard methods used in molecular systematics such as DNA extraction, PCR based methods (PCR-RFLP, AFLP, SSR), DNA purification, as well as cloning of PCR products (centrifuges, mixer mill, PCR thermocyclers, thermoblocks, incubators, PCR and flow boxes, spectrophotometer and fluorometer, temperature controlled electrophoresis apparatus, electrophoresis power supplies, blue light and UV-transilluminators with imaging system, etc.). The Institute owns or hires licenses for all relevant programs needed for molecular data evaluation (Geneious, PAUP, MacClade, SYN-TAX, SAS, DAx). 2. Laboratory of karyology and flow cytometry Regarding karyological research, the Institute possesses a karyological laboratory equipped by a microscope Axioscope 2 (Zeiss) and two flow cytometers equipped by a green laser with488 nm excitation wave and an HBO mercury arc lamp for UV excitation, respectively. Flow cytometers allow to detect relative (DNA ploidy level) as well as absolute DNA amount in plant material. Two cytometers running in parallel offer a possibility of simultaneous measurements of relative and absolute DNA amounts of the same sample and thus i.a. estimation of the proportion of AT/GC bases in the studied genome. 3. Morphometric laboratory All instrumental and software equipment required for the application of multivariate morphometrics is available. This consists of several high-quality stereomicroscopes (Olympus SZ 61) with digital cameras to output image to PC, and A3 scanner allowing observation, digitalization and subsequent evaluation of the investigated material. Software accessories comprise licenses of statistical programs and packages (SAS, SYN-TAX) needed for evaluation of the biostatistical data. 4. Mycological laboratory The analytical, genomic DNA extraction mycological laboratory serves for the analyses of lichen secondary chemistry and for the extraction of nucleic acids; innoculation and cultivation mycological laboratory for fungal culture preparation, and algological laboratory. 5. Mycological, phytopathological and algological cultivation labs The laboratories serve for isolation of the material from the substrate (microscopic fungi from host plant tissues, algae and cyanobacteria from water), inoculation and cultivation of the material for further analyses (e. g. molecular analyses). 6. Molecular Laboratory of Plant Physiology In our laboratories we use mainly the methods as a ROS determination, electrophoresis, root respiration, determination of different enzymes activities, methods for obtaining physiological status of investigated plants, gene expression and semiquantitative RT-PCR. 7. Pedological laboratory Chemical analyses of soil samples serve to complement datasets gathered for studies in plant communities. The results represent additional datasets for characterization of ecological requirements of particular plant assamblages.