The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Abstract

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

“…The genomes of B. rapa, B. oleracea and their allopolyploid offspring B. napus have been published recently [6][7][8] , and are often used to explain genome evolution in angiosperms [6][7][8] . The genomes of all Brassica species underwent a lineage-specific whole-genome triplication 6,7,9 , followed by diploidization that involved substantial genome reshuffling and gene losses 6,10-13 .…”

“…Table 15). Long terminal repeats (LTRs) are the predominant transposable element (TE) family identified in all sequenced Brassica genomes 6,7 . Copia-and Gypsy-type LTRs represent the two most abundant TE subfamilies.…”

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

“…However, as heterozygosity is likely to occur in regions it may be possible to collate information from several adjacent SNPs to define a region of heterozygosity. complex, sharing a whole genome triplication (Liu et al, 2014;Parkin et al, 2014;Wang et al, 2011), and the assembly of the recent Brassica C genome is of greater quality than the A genome assembly which was published three years earlier . While the chickpea genome reference is not perfect this relatively simple genome, produced using the latest sequencing chemistry and assembly methods is likely to have fewer misassembled regions than the Brassica genomes.…”

“…Genomic information is becoming increasingly available for Brassica and chickpea species. Proprietary genome sequences for B. napus and its diploid progenitor species were produced in 2009 (http://www.brassicagenome.net/), a public B. rapa genome was published in 2011 (Wang et al, 2011), the genome of B. oleracea (CC) was published recently (Liu et al, 2014;Parkin et al, 2014), and the genome of B. napus (AACC) is expected to become available in the next 12 months. Draft references of both kabuli and desi chickpea genomes were also published in 2013 (Jain et al, 2013;Varshney et al, 2013b).…”

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

“…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.…”