show Abstracthide AbstractIn this study we evaluate the impact of Bs on the transcriptome of the host genome; comparative analysis of rye with and without Bs was conducted. In addition, a wheat - rye B chromosome addition line was used to evaluate the effect of a B chromosome, which was added to a foreign host species. To ensure the comparability of the transcriptomes, we selected in both species anthers undergoing the first pollen mitosis for comparative RNA-seq.Our comparative RNA-seq analyses revealed that the presence of rye B chromosomes modulates the gene activity of the standard A chromosome complement of the natural host species rye and the alien host wheat. Thus, B encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes.