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Brassica napus , an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of  Brassica rapa  and  Brassica oleracea . Despite the economic importance of  B. napus , much is unresolved regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 183  B. napus  (including rapeseed, rutabaga, and Siberian kale), 112  B. rapa , and 62  B. oleracea  and its wild relatives. Using RNA-seq of  B. napus  accessions, we define the genetic diversity and sub-genome variance of six genetic clusters. Nuclear and organellar phylogenies for  B. napus  and its progenitors reveal varying patterns of inheritance and post-formation introgression. We discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for  B. napus  diversification. This study highlights the complex origin and evolution of  B. napus  providing insights that can further facilitate  B. napus  breeding and germplasm preservation.

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus