Abstract
BackgroundBrassica 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.ResultsWe 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.ConclusionOur 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 materialThe online version of this article (doi:10.1186/s12870-015-0417-5) contains supplementary material, which is available to authorized users.
Highlights
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
Digital gene expression (DGE) profile This research investigates the transcriptome profiling of diploids and spontaneous allopolyploids in Brassica by performing DGE analysis on the seeding stage of the six Brassica species, namely, B. rapa (Br), B. nigra (Bg), B. oleracea (Bo), B. napus (Bn), B. juncea (Bj), and B. carinata (Bc)
Clean tags were obtained after removing the low-quality sequences and adaptor sequences from the raw data. 6178564, 5881618, 6059222, 5964594, 6076830, and 5795234 clean tags were obtained in Br, Bg, Bo, Bn, Bj, and Bc, respectively
Summary
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. Many important economical crops are of polyploid origin, including wheat, cotton, and rapeseed [1]. Cruciferae includes the model species Arabidopsis thaliana and the economically important Brassica crops. These important crops include three diploid Brassica species, namely, B. rapa (AA, 2n = 20; Chinese cabbage, turnip, turnip rape), B. nigra (BB, 2n = 16; black mustard), and B. oleracea (CC, 2n = 18; cauliflower, broccoli, kale), and three allopolyploids spontaneously derived from pairwise hybridization of the diploids, which are B. napus (AACC, 2n = 38; oilseed rape, swede), B. juncea (AABB, 2n = 36; abyssinian or Ethiopian mustard), and B. carinata (BBCC, 2n = 34; Indian or brown mustard) [2].
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