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...

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin. (Résumé d'auteur