Domů Výzkum Oddělení DPDG Informace o oddělení Cytogenomika rostlin

Group of Cytogenomics

"No two plants are exactly alike. They are all different, and as a consequence, you have to know the difference."

Barbara McClintock

The Cytogenomics Group builds on the long-standing expertise in microscopy, cytogenetics, and genome biology at the Institute of Biophysics of the Czech Academy of Sciences, within the Department of Plant Developmental Genetics. Our research aims to uncover the genomic mechanisms that shape inheritance, genome stability, and evolutionary innovation in plants. By integrating cytogenetics, genomics, advanced imaging, and computational biology, we seek to identify the genomic and chromatin features that govern chromosome behavior, genome stability, and inheritance across generations.

Our research is centered around three major themes: (i) sex chromosome evolution, (ii) genomic plasticity associated with genome instability, and (iii) mechanisms of genetic inheritance in plants.

Sex chromosome evolution

Plant sex chromosomes evolved from pairs of autosomes and, compared with many animal systems, are evolutionarily young. Their remarkable genomic diversity and convergence provide an opportunity to uncover the processes that reshape chromosome architecture and drive the emergence and expansion of non-recombining regions.

Genomic plasticity associated with genome instability

Plant genomes display remarkable plasticity while maintaining accurate chromosome transmission across generations. Using Humulus lupulus as one of our models, we investigate how centromere organization and other genomic features influence chromosome segregation, segregation distortion, and ultimately genome integrity.

Mechanisms of genetic inheritance in plants

Meiosis generates haploid spores and reshuffles parental genomes, creating genetic diversity that is transmitted to subsequent generations. We investigate how chromosome organization, parental genomic contributions, and epigenetic regulation influence meiosis and gametogenesis, and how these mechanisms safeguard faithful genome transmission while generating new genetic variation.

Specifically, we investigate the three-dimensional organization of plant genomes using super-resolution microscopy (SIM² and STED) combined with advanced image analysis to reveal the spatial architecture of chromosomes and chromatin. By integrating optical genome mapping with artificial intelligence-assisted image analyses (ScanR), we characterize genome instability and identify genomic features that influence both classical and non-Mendelian inheritance. Furthermore, we employ cutting-edge chromatin profiling techniques, transcriptional analyses, and modern bioinformatic approaches to understand how genome organization regulates gene expression and drives plant development and evolution.


Selected publications

  • Bačovský V, Novotná P, Phillips D, Horáková L, Kružlicová J, Čížková J, Janoušek B, Čegan R. Sex chromosome pairing and multivalent associations during meiosis in diploid and polyploid Silene latifolia. Plant Physiol. 2026 Mar 2;200(3):kiaf599. doi: 10.1093/plphys/kiaf599.
  • Horáková L, Bačovský V, Čegan R, Janoušek B, Patzak J, Hobza R. Contrasting pattern of subtelomeric satellites in the Cannabaceae family. Front Plant Sci. 2025 Aug 19;16:1631369. doi: 10.3389/fpls.2025.1631369.
  • Kale SM, Gundlach H, Gericke O, Kamal N, Almeida A, Pitra N, Price N, Haberer G, Lux T, Krsticevic F, Kemp O, de Bang L, Himmelbach A, Padmarasu S, Rabanus-Wallace MT, Horáková L, Bačovský V, Nielsen K, Bjarnholt N, Micic N, Kruse-Andersen I, Møller BL, Janfelt C, Skadhauge B, Matthews PD, Mayer KFX, Stein N, Mascher M, Spannagl M, Feiner A, Braumann I. Extensive variation between chromosomes of North American and European hop. Nat Commun. 2026 May 27;17(1):4110. doi: 10.1038/s41467-026-72379-8.
  • Akagi T, Segawa T, Uchida R, Tanaka H, Shirasawa K, Yamagishi N, Yaegashi H, Natsume S, Takagi H, Abe A, Okuno M, Toyoda A, Sato K, Honniden Y, Zhang C, Ushijima K, Patzak J, Horáková L, Bačovský V, Hobza R, Charlesworth D, Itoh T, Ono E. Evolution and functioning of an X-A balance sex-determining system in hops. Nat Plants. 2025 Jul;11(7):1339-1352.
    doi: 10.1038/s41477-025-02017-6.
  • Horáková L, Jedlička P, Čegan R, Navrátilová P, Tanaka H, Toyoda A, Itoh T, Akagi T, Ono E, Hudzieczek V, Patzak J, Šafář J, Hobza R, Bačovský V. Dynamic patterns of repeats and retrotransposons in the centromeres of Humulus lupulus L. New Phytol. 2025 Sep;247(6):2766-2780. doi: 10.1111/nph.70380.
  • Sacchi B, Humphries Z, Kružlicová J, Bodláková M, Pyne C, Choudhury BI, Gong Y, Bačovský V, Hobza R, Barrett SCH, Wright SI. Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus. Mol Biol Evol. 2024 Apr 2;41(4):msae074. doi: 10.1093/molbev/msae074.

Preprints

  • Janicek T, Hudzieczek V, Polasek-Sedlackova H, Kratka M, Bacovsky V. Epigenetic reprogramming guides sexual dimorphism during floral development in Silene latifolia. bioRxiv 2025 Aug 30. doi: 10.1101/2025.08.26.672086.
  • Pascual-Díaz JP, Torres M, Bačovský V, Horáková L, Kružlicová J, Novotná P, Novoa A, Vitales D, Garcia S. Cytogenomic signatures of hybridisation in the genus Carpobrotus reveal biased parental dominance. bioRxiv 2026 Jul 4. doi: 10.64898/2026.07.03.736328.

Collaborations

  • Dr. Aline Muyle (Université de Montpellier, Montpellier) - sex chromosome evolution
  • Dr. Clément Lafon Placette (Charless University, Prague) - gene network analysis and diversity in seed characteristic
  • Prof. Stephen Wright (University of Toronto, Toronto) - sex chromosome evolution 
  • Dr. Dylan Phillips (Aberystwyth University, Aberystwyth) - meiosis in plants, tools to study meiotic features
  • Dr. Hana Polášek-Sedláčková (Institute of Biophysics, Brno) - development and utilisation of high-content imaging
  • Dr. Josef Patzak (Hop Research Institute, Žatec) - genome stability in hops
  • Dr. Jan Bartoš (Institute of Experimental Botany, Olomouc) - plant genomics and sequencing tools
  • Dr. Sònia Garcia (Institut Botànic de Barcelona, Barcelona) - sex chromosome evolution and biology of invasive species

The group members and contacts

We are a small, collaborative team, combining expertise in cytogenetics, genomics, microscopy, and computational biology. We study how genome architecture shapes inheritance and evolution in plants. If interested, please feel free to reach us!

Ing. Václav Bačovský, Ph.D.
(xbacovs@ibp.cz

Ing. Pavla Novotná
(novotna@ibp.cz)
Mgr. Lucie Horáková, Ph.D.
(lhorakova@ibp.cz)
 Mgr. Jana Kružlicová
(kruzlicova@ibp.cz)

 

Funding