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

Parkin, Isobel A. P., Koh, Chushin, Tang, Haibao, Robinson, Stephen J., Kagale, Sateesh, Clarke, Wayne E., Town, Chris D., Nixon, John, Krishnakumar, Vivek, Bidwell, Shelby L., Denoeud, France, Belcram, Harry, Links, Matthew G., Just, Jérémy, Clarke, Carling, Bender, Tricia, Huebert, Terry, Mason, Annaliese S., Pires, Chris J., Barker, Guy, Moore, Jonathan, Walley, Peter G., Manoli, Sahana, Batley, Jacqueline, Edwards, Dave, Nelson, Matthew N., Wang, Xiyin, Paterson, Andrew H., King, Graham, Bancroft, Ian, Chalhoub, Boulos and Sharpe, Andrew G. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology, 15 6: R77.1-R77.35. doi:10.1186/gb-2014-15-6-r77


Author Parkin, Isobel A. P.
Koh, Chushin
Tang, Haibao
Robinson, Stephen J.
Kagale, Sateesh
Clarke, Wayne E.
Town, Chris D.
Nixon, John
Krishnakumar, Vivek
Bidwell, Shelby L.
Denoeud, France
Belcram, Harry
Links, Matthew G.
Just, Jérémy
Clarke, Carling
Bender, Tricia
Huebert, Terry
Mason, Annaliese S.
Pires, Chris J.
Barker, Guy
Moore, Jonathan
Walley, Peter G.
Manoli, Sahana
Batley, Jacqueline
Edwards, Dave
Nelson, Matthew N.
Wang, Xiyin
Paterson, Andrew H.
King, Graham
Bancroft, Ian
Chalhoub, Boulos
Sharpe, Andrew G.
Title Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Formatted title
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-760X
Publication date 2014-06-10
Sub-type Article (original research)
DOI 10.1186/gb-2014-15-6-r77
Open Access Status DOI
Volume 15
Issue 6
Start page R77.1
End page R77.35
Total pages 35
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2015
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2015 Collection
 
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Citation counts: TR Web of Science Citation Count  Cited 51 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 56 times in Scopus Article | Citations
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Created: Fri, 20 Jun 2014, 10:40:39 EST by Annaliese Mason on behalf of School of Agriculture and Food Sciences