Oilseed rape (Brassica napus L.) was formed~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent A n and C n subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.T he Brassicaceae are a large eudicot family (1) and include the model plant Arabidopsis thaliana. Brassicas have a propensity for genome duplications ( Fig. 1) and genome mergers (2). They are major contributors to the human diet and were among the earliest cultigens (3).B. napus (genome A n A n C n C n ) was formed by recent allopolyploidy between ancestors of B. oleracea (Mediterranean cabbage, genome C o C o ) and B. rapa (Asian cabbage or turnip, genome A r A r ) and is polyphyletic (2, 4), with spontaneous formation regarded by Darwin as an example of unconscious selection (5). Cultivation began in Europe during the Middle Ages and spread worldwide. Diversifying selection gave rise to oilseed rape (canola), rutabaga, fodder rape, and kale morphotypes grown for oil, fodder, and food (4, 6).The homozygous B. napus genome of European winter oilseed cultivar 'Darmor-bzh' was assembled with long-read [>700 base pairs (bp)] 454 GS-FLX+ Titanium (Roche, Basel, Switzerland) and Sanger sequence (tables S1 to S5 and figs. S1 to S3) (7). Correction and gap filling used 79 Gb of Illumina (San Diego, CA) HiSeq sequence. A final assembly of 849.7 Mb was obtained with SOAP (8) and Newbler (Roche), with 89% nongapped sequence (tables S2 and S3). Unique mapping of 5× nonassembled 454 sequences from B. rapa ('Chiifu') or B. oleracea (' TO1000') assigned most of the 20,702 B. napus scaffolds to either the A n (8294) or the C n (9984) subgenomes (tables S4 and S5 and fig. S3). The assembly covers~79% of the 1130-Mb genome and includes 95.6% of Brassica expressed sequence tags (ESTs) (7). A single-nucleotide polymorphism (SNP) map (tables S6 to S9 and figs. S4 to S8) genetically anchored 712.3 Mb (84%) of the genome assembly, yielding pseudomolecules for the 19 chromosomes (table S10).The assembled C n subgenome (525.8 Mb) is larger than the A n subgenome (314.2 Mb), consistent with the relative sizes of the assembled C o genome of B. oleracea (540 Mb, 85% of thẽ 630-Mb genome) and the A r genome of B. rapa (312 Mb, 59% of the~530-Mb genome) (9-11). The B. napus assembly contains 34.8% transposable elements (TEs), less than the 40% estimated from raw reads (table...

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Most eukaryotes have genomes that exhibit high levels of gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1-to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the gene and organ examined. Remarkably, silencing and biased expression of some gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process.

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