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Background   Brassica rapa  is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops.    Results  To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two  B. rapa  subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the  B. rapa  pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of  Arabidopsis thaliana , which can be explained by the smaller effective population size of  B. rapa  due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three  B. rapa  morphotypes at approximately 250,000 YA, far predating  Brassica  domestication (5,000-10,000 YA).    Conclusions  By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three  B. rapa  morphotypes implies that prior to domestication there was already considerably divergence among  B. rapa  genotypes. Our study thus provides two new  B. rapa  reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in  B. rapa.Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.

Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage