Background and Aim: In Festuca pratensis, beside essential A chromosomes, 0 to 5 supernumerary B chromosomes (Bs) also have been reported in some genotypes. Although Bs are generally described as neutral with possibly negative effects on the host, there are some studies have shown the adaptive advantages of Bs containing plants under the unfavorable conditions. Based on previous reports that Bs increase allelic variation by altering the frequency and distribution of crossovers in A chromosome, they are not genetically inert and can affect regulatory mechanisms in the cell. Methods: In this study, the distribution pattern of repeats in the genome of F. pratensis individual plants possessing 0B (−B) or 2B chromosomes (+2B) was investigated using low pass Illumina sequencing and k-mer analysis. Comparative analysis of the reads of -B/+2B genotypes in RepeatExplorer pipeline identified the major repetitive sequences in A and B chromosomes. Consensus monomers of satellite and dispersed repeats were identified by TAREAN. Primers specific to B chromosome repeats were designed using primer3 and target amplicons were amplified by PCR. PCR products were labeled using the nick translation kit and used as probes in FISH experiments. Results: The results showed that repetitive sequences constituted 61.21% of nuclear genome of F. pratensis. The majority part of the repeatome was transposons that LTR retrotransposons accounted for 41% of repeats in the genome. Eighteen different satellite repeats were identified making up 3.9% of the genome among which two satellite were specific to the B chromosome of F. pratensis. FISH confirmed the presence of these specific repeats on B chromosomes. Conclusion: The identified B-specific tandem repeats can be used as a marker to trace the dynamics of supernumerary chromosomes and provide direct insight into the cellular basis of the B chromosome drive mechanism in F. pratensis. Our finding showed that although retrotransposons play a major role in the formation and evolution of the Festuca genome, satellite repeats also have a prominent presence in this plant.
