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...

The genome of the mesopolyploid crop species Brassica rapaThe Brassica rapa Genome Sequencing Project Consortium 1 Abstract:The Brassicaceae family which includes Arabidopsis thaliana, is a natural priority for reaching beyond botanical models to more deeply sample angiosperm genomic and functional diversity. Here we report the draft genome sequence and its annoation of Brassica rapa, one of the two ancestral species of oilseed rape. We modeled 41,174 protein-coding genes in the B. rapa genome. B. rapa has experienced only the second genome triplication reported to date, with its close relationship to A. thaliana providing a useful outgroup for investigating many consequences of triplication for its structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one copy containing a greater proportion of genes expected to have been present in its ancestor (70%) than the remaining two (46% and 36%). Both a generally rapid evolutionary rate, and specific copy number amplifications of particular gene families, may contribute to the remarkable propensity of Brassica species for the development of new morphological variants. The B. rapa genome provides a new resource for comparative and evolutionary analysis of the Brassicaceae genomes and also a platform for genetic improvement of Brassica oil and vegetable crops.2

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.