Šimková Group

     The major aim of our group is dissecting complex genomes of small grain cereals on both structural and functional level. Our approaches mostly exploit our lab’s unique pipeline for chromosome sorting and use it to reduce genome complexity and overcome problems due to polyploidy.  On this principle, we built a complete set of chromosome-specific BAC libraries including each chromosome arm of the bread wheat genome. We focused on one of them – the short arm of wheat chromosome 7D – and tackled it by multiple techniques, including physical mapping, BAC-by-BAC sequencing and optical mapping. The obtained data were applied in generating bread wheat reference sequence by the IWGSC, cloning a Russian wheat aphid resistance gene and analyses of challenging regions of the 7DS, including tandem repeats and the centromere.
     Our current research targets multigene ribosomal RNA loci in several Triticeae species. We are approaching them by the combination of chromosome sorting, optical mapping, long-read nanopore sequencing and RNA-seq aiming to clarify their expression and evolution. Another adopted technique is the Hi-C, a chromatin-conformation-capture-based method that helped us localize missing rDNA arrays in genome assemblies. Besides, we use the Hi-C to clarify chromatin packaging in mitotic chromosomes and interphase nuclei of barley and rice, respectively. Our plans for the future include analyses of three-dimensional organisation of the cereal genomes as well as of chromatin characteristics affecting their gene expression.