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

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DOIResolve DOI: http://doi.org/10.1186/gb-2014-15-6-r77
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TypeArticle
Journal titleGenome Biology
ISSN1474-7596
Volume15
Issue6
Article numberR77
SubjectBrassica oleracea; Brassica rapa; controlled study; DNA methylation; gene dosage; gene expression; gene mapping; genome size; hexaploidy; plant genome; plant leaf; polyploidy; transcriptomics; Brassica oleracea
AbstractBackground: Brassica 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. Results: We 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. Conclusions: Differential 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.
Publication date
PublisherBioMed Central
LanguageEnglish
AffiliationNational Research Council Canada; Aquatic and Crop Resource Development
Peer reviewedYes
NPARC number21275559
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Record identifier30346eb8-00f2-4fe5-9745-8a4d4e9d5b8d
Record created2015-07-14
Record modified2016-05-09
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