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The aneuploidy chromosome addition lines with individual chromosomes of one species into the whole genome of another species developed from interspecific or intergeneric crosses are ideal for studying the gene expression regulation under asymmetrical genome interactions. Here, we chose two rapeseed-radish addition lines (2n=40, AACC+2R) with all chromosomes of rapeseed and one pair of radish chromosomes carrying 25S rDNA loci and both 5S and 25S rDNA loci, respectively. Transcriptome sequencing of these two rapeseed-radish addition lines, together with two parents (Brassica napus, 2n=38, AACC; Raphanus sativus, 2n=18, RR), was performed to assess gene expression changes due to the aneuploidy effect. Our results showed that the global gene expression perturbations in two addition lines showed asymmetric distributions between A and C subgenomes, for more downregulated genes located in the C subgenome. Moreover, several dysregulated domains occurred in the addition lines and majority of them were clustered in C subgenome, further revealing that C subgenome was more inclined to be repressed by the aneuploidy. Homoeolog expression was slightly biased toward C subgenome in the parent B. napus, but had no preference to either of A or C subgenome in the addition lines. The total number of biased genes increased sharply and most of them were shared only by two addition lines, indicating that aneuploidy could change the extent and direction of homoeolog expression. The triplicated subgenomes which were orthologs to the chromosomes of Arabidopsis thaliana also exhibited dramatic alternations in two additions. Together, our results revealed that the addition of individual radish chromosomes could induce dramatically transcriptomic disturbances and those expression changes gave asymmetric distributions between two subgenomes in B. napus. The possible mechanisms including the uniparental expression of rRNA genes in the allopolyploids and additions for the findings are discussed. [ABSTRACT FROM AUTHOR]