BACKGROUND: Supernumerary chromosomes have been found in many organisms. In 
fungi, these "accessory" or "dispensable" chromosomes are present at different 
frequencies in populations and are usually characterized by higher repetitive 
DNA content and lower gene density when compared to the core chromosomes. In the 
reference strain of the wheat pathogen, Zymoseptoria tritici, eight discrete 
accessory chromosomes have been found. So far, no functional role has been 
assigned to these chromosomes; however, they have existed as separate entities 
in the karyotypes of Zymoseptoria species over evolutionary time. In this study, 
we addressed what-if anything-distinguishes the chromatin of accessory 
chromosomes from core chromosomes. We used chromatin immunoprecipitation 
combined with high-throughput sequencing ("ChIP-seq") of DNA associated with the 
centromere-specific histone H3, CENP-A (CenH3), to identify centromeric DNA, and 
ChIP-seq with antibodies against dimethylated H3K4, trimethylated H3K9 and 
trimethylated H3K27 to determine the relative distribution and proportion of 
euchromatin, obligate and facultative heterochromatin, respectively.
RESULTS: Centromeres of the eight accessory chromosomes have the same sequence 
composition and structure as centromeres of the 13 core chromosomes and they are 
of similar length. Unlike those of most other fungi, Z. tritici centromeres are 
not composed entirely of repetitive DNA; some centromeres contain only unique 
DNA sequences, and bona fide expressed genes are located in regions enriched 
with CenH3. By fluorescence microscopy, we showed that centromeres of Z. tritici 
do not cluster into a single chromocenter during interphase. We found 
dramatically higher enrichment of H3K9me3 and H3K27me3 on the accessory 
chromosomes, consistent with the twofold higher proportion of repetitive DNA and 
poorly transcribed genes. In contrast, no single histone modification tested 
here correlated with the distribution of centromeric nucleosomes.
CONCLUSIONS: All centromeres are similar in length and composed of a mixture of 
unique and repeat DNA, and most contain actively transcribed genes. Centromeres, 
subtelomeric regions or telomere repeat length cannot account for the 
differences in transfer fidelity between core and accessory chromosomes, but 
accessory chromosomes are greatly enriched in nucleosomes with H3K27 
trimethylation. Genes on accessory chromosomes appear to be silenced by 
trimethylation of H3K9 and H3K27.