Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

Abstract

BackgroundBrassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.ResultsWe generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event.ConclusionsDifferential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.

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).…”

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

“…Neopolyploids being recent polyploids contain clearly distinguishable subgenomes (Kagale et al, 2014). In comparison, the parental subgenomes in mesopolyploids are only discernible by comparative genetic and genomic approaches (Parkin et al, 2005;Mandáková et al, 2010b;Parkin et al, 2014), which is not possible in paleopolyploids where long-term genome restructuring leads to the assimilation of parental subgenomes (Mandáková et al, 2010b).…”

“…Using Bayesian approaches and fossil information as age constraints, the age of the triplication event has now been estimated to be 22.5 million years (Beilstein et al, 2010). Similarly, recent genome sequencing of Leavenworthia alabamica (Haudry et al, 2013), Camelina sativa (Kagale et al, 2014), and Brassica oleracea (Liu et al, 2014;Parkin et al, 2014) have uncovered more recent neo/mesopolyploidy events that formed the basis for the evolution of their hexaploid genomes. Comparative cytogenetic and molecular phylogenetic analyses have unveiled additional mesopolyploidy events in a few Australian and New Zealand crucifer genera belonging to the Microlepidieae and Heliophileae tribes that are endemic to Namibia and South Africa (Joly et al, 2009;Mandáková et al, 2010aMandáková et al, , 2010bMandáková et al, , 2012, implying a key role for recurring mesopolyploidy events in the diversification of the Brassicaceae.…”

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

“…The whole genome sequences of B. rapa [12], B. nigra [13], B. oleracea [14,15], B. juncea [13] and B. napus [16] were used. The reverse transcriptase core domain region from the A. thaliana ONSEN copies were used as a query in the homology search by BLAST server of NCBI and Phytozome ver 10 [35].…”