In various eukaryotes, supernumerary B chromosomes (Bs) are an optional genomic component. The notable features of Bs are variability in numbers among individuals, species-specific organization, and enrichments with different types of repetitive DNA; and the inheritance of the B chromosome is not subject to Mendelian laws. The origin of Bs is still obscure, but studies employing recent advances in next-generation sequencing indicate that they arise as a result of A chromosome rearrangements, and some genes of standard A chromosomes remain transcriptionally active in Bs.

In the present study, the impact of Bs on the current changes in the genome of goatgrass, Aegilops speltoides, which is a wild progenitor of the B and G genomes of allopolyploid wheats, was addressed. We focused on the cytogenetic features of Bs and the intra-organismal copy number dynamics of retrotransposons (TEs) and species-specific tandem repeat (TR) in plants with and without Bs in highly heterogeneous populations of Ae. speltoides. Our data indicate that fluctuations in TE and TR copy numbers are associated with DNA damage and repair processes during cell proliferation and differentiation, and ectopic recombination is one of the mechanisms by which Bs play a role in genome changes.