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Šimková Group

     The major aim of our group is to dissect complex genomes of small grain cereals at both structural and functional level. Our approaches frequently exploit our lab’s unique pipeline for chromosome and nuclei flow sorting and a well-established technique of optical mapping. Capitalising on these technologies, we aided in generating reference genomes of several crop species, contributed to cloning a Russian wheat aphid resistance gene and revealed the fine structure and dynamic transcription of ribosomal DNA loci in bread wheat and barley. Besides, we adopted the chromatin-conformation-capture technique Hi-C to study chromatin packaging during the cell cycle and, complemented by a variety of epigenetic techniques, to map cis-regulatory elements controlling transcription during barley development.
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News

  • November 2024: A paper of Jianyong Chen called The genetic mechanism of B chromosome drive in rye illuminated by chromosome-scale assembly with Hanka's and Zuzka's contribution is online! It has been published in Nature Communications!!! Congratulations!
  • October 2024: The first oficial meeting of Work package 1 of a project TowArds Next GENeration Crops of the ERDF Programme Johannes Amos Comenius was organized at our Institute. Hanka, who is also a formal leader of the package, Pavla, Zuzka and Ondra met all of their colaborators and were informed about progress of all working groups belonging to the package.
  • October 2024: Zuzka, Šimon and Ondra were members of group of people who presented our Institute to a public in Flora Hortikomplex 2024.   
  • September 2024: Ondřej Kopecký has joined our group as a Ph.D. student. Welcome and good luck!
  • September 2024: A paper of Kitti Szöke-Pázsi on DArTseq genotyping with Zuzka's contribution was published in Frontiers in Plant Science. 
  • May 2024: Pavla's student Veronika has successfully defended her diploma thesis. Congratulations and good luck in a future career!
  • March 2024: New Hanka's paper about Hi-C techniques has been published in Journal of Experimental Botany. 
  • January 2024: Helena has returned from her maternity leave. Welcome back!
  • December 2023: Šimon's first paper is online now! A story dedicated to promoterome of barley embryo has been published in Computational and Structural Biotechnology Journal. Congratulations Šimon!
  • November 2023: Hanka's chapter Wheat Chromosomal resources and their role in wheat research was published in a book The Wheat Genome, which is a part of the book series Compendium of Plant Genome. 

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Vacancies

Group members

Leader
Hana Šimková Ph.D.
Postdoc
Pavla Navrátilová Ph.D.
Postdoc
Helena Toegelová Ph.D.
Postdoc
Zuzana Tulpová Ph.D.
Ph.D. student
Šimon Pavlů Msc.
Ph.D. student
Ondřej Kopecký Msc.

Projects

Genome-wide mapping of cis-regulatory elements controlling transcription . . .
Leader
Hana Šimková Ph.D.
Gene transcription is controlled by interplay of transcription factors and non-coding cis-regulatory elements (CREs) - promoters, enhancers and silencers. Since association mapping in maize indicated connection of putative CREs with expression QTLs for important traits, localization of these elements and linking them to their target genes become a vital background for crop breeding and bioengineering. In the project, we aim to precisely delimit and . . .
Dynamics and evolution of multigene ribosomal RNA loci in Triticeae
Leader
Hana Šimková Ph.D
Ribosomal RNA gene loci (rDNA) have been among extensively studied components of eukaryotic genomes. They were shown to be associated with nucleolus, the largest functional domain of the nucleus and the site of ribosomal biogenesis.  Despite the biological importance, detailed information on molecular organization of rDNA regions is missing, especially in plants. This is mainly due to structure of rDNA loci, which are organized as long arrays of . . .
MITOCHROM: Three-dimensional organization of nuclear chromatin in plants . . .
Leader
Prof. Jaroslav Doležel
Recent methodological advances provided novel insights into the spatial genome organization in mammalian cell nuclei and its functional role. This progress contrasts with the limited knowledge on higher order chromatin folding in mitotic chromosomes. Our preliminary data on chromatin contact frequency at megabase resolution obtained in barley mitotic chromosomes suggest remarkable differences in mitotic chromosome organization between . . .

Publications