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

Isobel AP Parkin1*, Chushin Koh2, Haibao Tang3, Stephen J Robinson1, Sateesh Kagale12, Wayne E Clarke1, Chris D Town3, John Nixon1, Vivek Krishnakumar3, Shelby L Bidwell3, France Denoeud456, Harry Belcram7, Matthew G Links1, Jérémy Just7, Carling Clarke2, Tricia Bender1, Terry Huebert1, Annaliese S Mason8, J Chris Pires9, Guy Barker10, Jonathan Moore10, Peter G Walley10, Sahana Manoli8, Jacqueline Batley8, David Edwards8, Matthew N Nelson11, Xiyin Wang12, Andrew H Paterson12, Graham King13, Ian Bancroft14, Boulos Chalhoub7* and Andrew G Sharpe2*

Author Affiliations

1 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N0X2, Canada

2 National Research Council Canada, 110 Gymnasium Place, Saskatoon S7N0W9, Canada

3 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

4 Commissariat à l’Energie Atomique (CEA), Institut de Génomique, BP5706, Evry, 91057, France

5 Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry, France

6 Université d’Evry, UMR 8030, Evry, CP5706, France

7 Organization and Evolution of Plant Genomes, Unité de Recherche en Génomique Végétale, Unité Mixte de Rechercheé 1165, (Inland Northwest Research Alliance Institut National de Recherche Agronomique - Centre National de la Recherche Scientifique, Université Evry Val d’Essonne), Evry, France

8 School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia

9 Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA

10 Warwick Life Sciences, The University of Warwick, Warwick CV35 9EF, UK

11 School of Plant Biology/ The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

12 Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA

13 Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia

14 Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK

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Genome Biology 2014, 15:R77  doi:10.1186/gb-2014-15-6-r77

Published: 10 June 2014

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.