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Background   Brassica  includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U’s triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale.    Results  We examined the gene expression patterns of three diploids ( Brassica rapa ,  B. nigra , and  B. oleracea ) and three amphidiploids ( B. napus ,  B. juncea , and  B. carinata ) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547–21995 genes of  B. rapa  genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in  Brassica  amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in  Brassica  species.    Conclusion  Our results provided an understanding of the transcriptome complexity of natural  Brassica  species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among  Brassica  species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0417-5) contains supplementary material, which is available to authorized users.

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids