Laboratory of Molecular Cytogenetics and Cytometry opens new PhD positions.
Sequencing and annotation of chromosome arm 3DS of hexaploid wheat
The project (GAČR P501/12/G090) is focused on the study of evolution and function of complex plant genomes. The aim of the Ph.D. study is to BAC-by-BAC sequence, assembly and annotate chromosome arm 3DS of hexaploid wheat. Ph.D. student will be responsible for assembly of individual BAC clones of the physical map of the chromosome arm. Annotation will be done in two steps: first, automated annotation will be done using TriAnnot pipeline; second, annotation will be manually curated on the BAC by BAC basis. Stay at INRA (Clermont-Ferrand) is pre-arranged with one of the best specialists in the field (Dr. Catherine Feuillet).
Supervisor: Jan Bartoš, Ph.D.
Study of tissue-specific expression in hexaploid wheat
The project (GAČR P501/12/G090) is focused on the study of evolution and function of complex plant genomes. The aim of the Ph.D. study is to understand interactions of homoeologous genomes in different cell types and their changes during plat development. Ph.D. Student will identify tissue-specific promoters and prepare constructs for GFP under their control. Promoter activity will be confirmed using fluorescent microscopy after transformation. Tissue-specific cell will be then sorted after protoplast isolation based on fluorescence of GFP. RNA-Seq will be used to follow the expression of individual transcripts. Stay at University of Arizona (Tucson, USA) is pre-arranged with one of the best specialist in the field (Dr. David W. Galbraith).
Supervisor: Jan Bartoš, Ph.D.
Plant genome analysis using flow,sorted chromosomes
The analysis of plant genomes is hampered by prevalence of repetitive DNA and in some cases also by polyploidy. During the last decade, a novel approach has been developed to overcome the difficulty by dissecting the genomes to individual chromosomes and led to the establishment of chromosome genomics in several important crops. The aim of the Ph.D. study is to further enhance the potential of chromosome genomics. In order to overcome the current limitation of chromosome flow sorting to only some chromosomes in a karyotype, the PhD candidate will explore possibilities for labeling specific chromosomes using suitable probes. Two approaches will be used. The first will involve fluorescently labeled polyamides, which bind the minor groove of DNA and are capable of sequence selective recognition. The second approach will use TALE (transcription activator-like effectors) DNA binding domains fused to fluorescent proteins. A secondment has been pre-arranged at the University of Minnesota (Minneapolis) in the laboratory of Prof. Daniel Voytas who has pioneered the use of TAL effectors for DNA targeting.
Supervisor: Doc. Ing. Jaroslav Doležel, DrSc.
Genetic aspects of heavy metal uptake in barley
Toxic concentrations of heavy metals in soil have been caused recently by activities of man. Moreover, metals such as Cd and As are known as potent toxins and carcinogens in humans and as pollutants effectively accumulate throughout the food chain. Many plant species evolved genetic mechanisms increasing the ability to tolerate metal contamination by different detoxification processes and removal of a metal from the plant. The aim of the Ph.D. study is to characterize new candidate genes for metal transport in metal hypertolerant species from genus Silene. In parallel, the genes revealing relation to metal tolerance will be studied in barley species. Comparison of next generation based transcriptome databases will enable to decipher common and unique genetic pathways between species and populations. Finally, reverse genetics experiments will confirm the ability of individual genes to modulate metal uptake and detoxification in barley.
Supervisor: Roman Hobza, Ph.D.
Sex chromosome evolution in plants
In contrast to animals with mostly separated two sexes, a number of reproductive strategies coexist in higher plants. Surprisingly, the presence of well-established sex chromosomes in dioecious plants is rare. We intend to investigate structure and evolution of sex chromosomes in dioecious plant Silene latifolia (human-like sex determination) and Rumex acetosa (Drosophila-like sex determination). Compared to human, these species present a unique model to study early stages of sex chromosome evolution. Since only limited sequence information on sex chromosomes is available in these species we focus on characterization of X chromosome as the fundamental step towards understanding the evolution of sex chromosomes. We will employ methods of chromosome-specific genomics to construct physical map of the X chromosome. Subsequently, we will generate expression data for individual tissues, sexes and species based on RNA-seq approach. Comparative analysis of individual genes with expression data will reveal functional aspects of sex chromosomes evolution. Further, our data will help to decipher degenerative processes in Y chromosome evolution.
Supervisor: Roman Hobza, Ph.D.
Analysis of diversity and evolution of satellite DNA in Festuca sp. and Lolium spp. and in their interspecific hybrids
A recent study on nuclear genome structure of Festuca spp. revealed a presence of different types of satellite DNA sequences, including sequences with 1 – 2 kb long repetitive units. The aim of the Ph.D. study will be to further enhance the knowledge of the role and evolution of satellite DNA sequences in nuclear genomes of grass species and their interspecific hybrids. Ph.D. student will identify specific types of satellite DNA sequences in the genomes and their individual chromosomes respectively, using the Illumina sequencing. In parallel, genomic organization of the satellite repeats will be determined using fluorescence in situ hybridization (FISH) on metaphase chromosomes and interphase nuclei. A stay at the University of California (Riverside, USA) has been pre-arranged with Prof. Adam Lukaszewski.
Supervisor: Eva Hřibová, Ph.D.
Modelling of nuclei 3D structure in wide hybrids
In interphase nuclei, individual chromosomes are located in so called chromosome domains. However, the position of such domains occupied by homologous or homoeologous chromosomes in polyploids is largely unknown. This is mainly due to inability to “paint” (detect) whole chromosomes. In our laboratory, we have recently developed unique plant material for such research project. The main aim of the Ph.D. study will be an optimization of 3D-FISH protocol and confocal microscopy for initial data set mining. If progressing well, the student will use the cutting edge bioinformatic tools for interpretation of the data obtained during the project. Stay at Cornell University (NY, USA) is pre-arranged with one of the best specialists in the field (Dr. Wojtek Pawlowski).
Supervisor: David Kopecký, Ph.D.
Fine mapping and gene analysis of the flowering time gene in wheat
The project (GAČR P501/10/1178) focuses on the study of wheat flowering time gene. The aim of the project is preparation of fine genetic map for map-based cloning of the gene influencing heading time in wheat. Student will be responsible for genotyping and phenotyping of mapping population, enlargement of the population, development of new markers and selection of candidate genes for functional validation. Stay at JIC (John Innes Centre, Great Britain) is pre-arranged with one of the best specialist in the field (prof. J.W. Snape).
Supervisor: RNDr. Jan Šafář, Ph.D.
Organization of DNA in interphase nuclei and mitotic chromosomes of plants
The organization of DNA in chromatin of interphase nuclei and mitotic chromosomes plays a key role in genome function, including gene expression and faithful transfer of hereditary information to daughter cells and progeny. The aim of the Ph.D. study will be to elucidate three dimensional organization of DNA in plant mitotic chromosomes and interphase nuclei. The so-called Hi-C technology will be used to measure the interaction frequency between specific regions of the genome. This information will be used to computationally model and analyse three-dimensional chromatin organization and produce a model of a plant mitotic and interphase chromosome. The same approach will be used to model interaction of various chromosomes within cell nuclei. The data will be supported by 3D fluorescence in situ hybridization. Stay at McGill University (Montreal, Canada) is pre-arranged with one of the leaders in this area of research (Prof. Josee Dostie).
Supervisor: Ing. Hana Šimková, CSc.
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