Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Abstract

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...

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…At least 64.8% of the assembled genome are transposable elements (TEs), which was substantially higher than that in canola (>34.8%) 9 , but lower than in wheat (>76.6%) 6 . Although the total content of TEs was similar to that present in a second G. hirsutum draft genome 28 (64.8% versus 66%), the retrotransposon frequencies were different (52.29% versus 62.81%).…”

“…We have developed an integrated approach to the sequencing and assembly of an allopolyploid cotton genome that could be applied to the sequencing of complex genomes of other polyploid crops. In contrast to recently formed allopolyploids such as wheat 6 and canola 9 , the allopolyploid cotton genome has features of asymmetrical evolution. This sequence of an allotetraploid cotton line, together with genetically mapped QTLs and ~5 million SNPs between G. hirsutum and G. barbadense, provide genomic resources for map-based cloning, germplasm improvement and genomic selection in cotton lines to help meet the growing demand for renewable fiber, oil and fuel.…”

“…Some other allopolyploids, such as cotton 24 and Arabidopsis 25 , do not show many changes in their genomic sequences. Recent genome sequencing studies revealed a relatively stable genome organization in cultivated hexaploid wheat 6 and Brassica napus 9 . This is probably because the exact progenitors that could form stable cultivated allopolyploids were lost.…”

“…However, chromosome sorting is less useful for cotton, which has a large number of small chromosomes (2n = 4x = 52). A conventional approach is to sequence diploid progenitor genomes, which can then guide the assembly of homoeologous chromosomes of allopolyploids, as was done for Brassica napus [7][8][9] . One problem with this approach is that many sequence contigs and scaffolds remain ambiguous with respect to homoeologous relationships.…”

“…Texas Marker-1 (TM-1), which is widely used as a genetic standard 1,10 . We generated a genome sequence containing two-to about fourfold longer sequence scaffolds (N50 = 1,600 kb) than that produced for other allopolyploid species Brassica napus (N50 = 764 kb) 9 , Nicotiana tabacum sequencing of allotetraploid cotton (Gossypium hirsutum l. acc. tM-1) provides a resource for fiber improvement A r t i c l e s (N50 = 345~386 kb) 11 and wheat (contig N50 = 515~4,297 bp) 6 , as well as the extant diploid A-genome progenitor of G. arboreum (N50 = 666 kb) 2 (N50, the size above which 50% of the total length of the sequence assembly can be found).…”