Epigenetics of the plant pathogen Zymoseptoria tritici

The genome of the fungal wheat pathogen Zymoseptoria tritici consists of thirteen essential chromosomes and several so-called dispensable chromosomes. These dispensable chromosomes encode only 6% of the protein coding genes of Z. tritici. To date no genes involved in pathogenicity are described on t...

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Bibliographic Details
Main Author: Schotanus, Klaas
Contributors: Stukenbrock, Eva H. (Prof.Dr.) (Thesis advisor)
Format: Dissertation
Language:English
Published: Philipps-Universität Marburg 2014
Biologie
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Summary:The genome of the fungal wheat pathogen Zymoseptoria tritici consists of thirteen essential chromosomes and several so-called dispensable chromosomes. These dispensable chromosomes encode only 6% of the protein coding genes of Z. tritici. To date no genes involved in pathogenicity are described on the dispensable chromosomes which can be lost after meiosis or mitotic cell division without any apparent effect on fitness. To investigate the underlying molecular basis of instability of the dispensable chromosomes, the epigenetic components of both the essential and dispensable chromosomes were characterized here. Chromatin immunoprecipitation and sequencing of DNA associated with the centromere specific histone (CenH3) was conducted to identify the centromeres of Z. tritici. It was shown that the centromeres of Z. tritici are small, sequence independent and lack any conserved motif. The centromeres are AT-rich, but not located in the most abundant AT-rich region of the chromosomes, and the centromeric organization is similar for both essential and dispensable chromosomes. To study centromere dynamic, parental and progeny strains derived from a meiotic cross were included in the study. The centromeres of these strains were shown to be conserved among Z. tritici strains. The deletion of the centromere of the dispensable chromosome 14 resulted in several strains were chromosome 14 was completely lost, while only a single strain was identified with a neocentromere on chromosome 14. The chromatin content of both types of chromosomes was also investigated. Three histone modifications specific for either euchromatin or heterochromatin were characterized. The essential chromosomes are enriched with euchromatin while the dispensable chromosomes are mainly heterochromatic. Several repeat rich regions with low gene density were also enriched with heterochromatin on the essential chromosomes. One particularly large region of 780 kb of the essential chromosome 7 was in addition found to be enriched with facultative heterochromatin. Genes in this region are silenced both during axenic and infectious growth. Based on the obtained results, it can be concluded that the difference between the essential and dispensable chromosomes cannot be associated with the centromeres. However, differences in the chromatin states is a main difference between the two types of chromosomes. To investigate the hemibiotrophic lifestyle switch in Z. tritici the epigenetic component of infectious growth was studied with a focus on RNA interference (RNAi). Five mutant strains of several proteins involved in the RNAi pathway were created. It could be demonstrated that Dicer and Argonaute genes play a role during the formation of asexual fruiting bodies called pycnidia. In contrast to the Dicer gene, the Argonaute genes show an unusual degree of sequence variation among Z. tritici strains. Collectively, the work presented here underlines the importance of epigenetics in both genome stability as well as pathogenicity in the fungal pathogen Z. tritici.
DOI:https://doi.org/10.17192/z2015.0083