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Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
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(2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology, Volume 15 (Number 6). Article number R77. doi:10.1186/gb-2014-15-6-r77 ISSN 1474-7596.
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Official URL: http://dx.doi.org/10.1186/gb-2014-15-6-r77
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.
Item Type: | Journal Article | ||||||||
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Alternative Title: | |||||||||
Subjects: | Q Science > QK Botany S Agriculture > SB Plant culture |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
Library of Congress Subject Headings (LCSH): | Cole crops , Plant genomes | ||||||||
Journal or Publication Title: | Genome Biology | ||||||||
Publisher: | BioMed Central Ltd. | ||||||||
ISSN: | 1474-7596 | ||||||||
Official Date: | 10 June 2014 | ||||||||
Dates: |
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Volume: | Volume 15 | ||||||||
Number: | Number 6 | ||||||||
Article Number: | Article number R77 | ||||||||
DOI: | 10.1186/gb-2014-15-6-r77 | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 27 December 2015 | ||||||||
Date of first compliant Open Access: | 27 December 2015 | ||||||||
Funder: | Canadian Canola Sequencing Initiative (CanSeq), Genome Alberta, Agricultural Flexibility Fund (Agri-Flex, AAFC), National Science Foundation (U.S.) (NSF), Australian Research Council (ARC), Australian Genome Research Facility (AGRF), Queensland Cyber Infrastructure Foundation (QCIF), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Great Britain. Department for Environment, Food and Rural Affairs (DEFRA) | ||||||||
Grant number: | 0638536 (NSF), BB/E017363/1 (BBSRC), IF0157 (DEFRA) |
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