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Background   Brassica juncea  is an economically important vegetable crop in China, oil crop in India, condiment crop in Europe and selected for canola quality recently in Canada and Australia.  B. juncea  (2n = 36, AABB) is an allotetraploid derived from interspecific hybridization between  B. rapa  (2n = 20, AA) and  B. nigra  (2n = 16, BB), followed by spontaneous chromosome doubling.    Results  Comparative genome analysis by genome survey sequence (GSS) of allopolyploid  B. juncea  with  B. rapa  was carried out based on high-throughput sequencing approaches. Over 28.35 Gb of GSS data were used for comparative analysis of  B. juncea  and  B. rapa , producing 45.93% reads mapping to the  B. rapa  genome with a high ratio of single-end reads. Mapping data suggested more structure variation (SV) in the  B. juncea  genome than in  B. rapa . We detected 2,921,310 single nucleotide polymorphisms (SNPs) with high heterozygosity and 113,368 SVs, including 1-3 bp Indels, between  B. juncea  and  B. rapa . Non-synonymous polymorphisms in glucosinolate biosynthesis genes may account for differences in glucosinolate biosynthesis and glucosinolate components between  B. juncea  and  B. rapa . Furthermore, we identified distinctive vernalization-dependent and photoperiod-dependent flowering pathways coexisting in allopolyploid  B. juncea , suggesting contribution of these pathways to adaptation for survival during polyploidization.    Conclusions  Taken together, we proposed that polyploidization has allowed for accelerated evolution of the glucosinolate biosynthesis and flowering pathways in  B. juncea  that likely permit the phenotypic variation observed in the crop.

Genome survey sequencing provides clues into glucosinolate biosynthesis and flowering pathway evolution in allotetrapolyploid Brassica juncea