Pulsed-field gel electrophoresis was used to generate electrophoretic karyotypes for 15 strains representing the three closely related plant-pathogenic fungi Rhynchosporium commune, R. secalis and R. agropyri. Between 13 and 16 chromosomes ranging in size from 0.9 to 6.4 Mb were found among the strains, leading to estimated genome sizes ranging from 54 to 63 Mb. Southern hybridization was used to identify homologous chromosomes, allowing detection of chromosome-length polymorphisms. There were no obvious differences in genome sizes or structures among the three species. The avirulence gene NIP1 is present on a large chromosome that is not likely to be dispensable. Two strains of R. commune that were proposed in earlier studies to be aneuploid as a result of a parasexual cycle did not possess a larger number of chromosomes. The reported information on genome size and chromosome number will be useful for genome sequencing projects that aim to identify genes involved in speciation and host specialization.
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