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

Research output: Contribution to journalArticle

Published copy (DOI)

Author(s)

  • Isobel Ap Parkin
  • Chushin Koh
  • Haibao Tang
  • Stephen J Robinson
  • Sateesh Kagale
  • Wayne E Clarke
  • Chris D Town
  • John Nixon
  • Vivek Krishnakumar
  • Shelby L Bidwell
  • France Denoeud
  • Harry Belcram
  • Matthew G Links
  • Jérémy Just
  • Carling Clarke
  • Tricia Bender
  • Terry Huebert
  • Annaliese S Mason
  • Chris J Pires
  • Guy Barker
  • Jonathan Moore
  • Peter G Walley
  • Sahana Manoli
  • Jacqueline Batley
  • Dave Edwards
  • Matthew N Nelson
  • Xiyin Wang
  • Andrew H Paterson
  • Graham King
  • Boulos Chalhoub
  • Andrew G Sharpe

Department/unit(s)

Publication details

JournalGenome biology
DatePublished - 10 Jun 2014
Issue number6
Volume15
Original languageEnglish

Abstract

BACKGROUND: 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.

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