By the same authors

From the same journal

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

Research output: Contribution to journalArticlepeer-review

Standard

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. / Parkin, Isobel Ap; 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.

In: Genome biology, Vol. 15, No. 6, R77, 10.06.2014.

Research output: Contribution to journalArticlepeer-review

Harvard

Parkin, IA, Koh, C, Tang, H, Robinson, SJ, Kagale, S, Clarke, WE, Town, CD, Nixon, J, Krishnakumar, V, Bidwell, SL, Denoeud, F, Belcram, H, Links, MG, Just, J, Clarke, C, Bender, T, Huebert, T, Mason, AS, Pires, CJ, Barker, G, Moore, J, Walley, PG, Manoli, S, Batley, J, Edwards, D, Nelson, MN, Wang, X, Paterson, AH, King, G, Bancroft, I, Chalhoub, B & Sharpe, AG 2014, 'Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea', Genome biology, vol. 15, no. 6, R77. https://doi.org/10.1186/gb-2014-15-6-r77

APA

Parkin, I. A., Koh, C., Tang, H., Robinson, S. J., Kagale, S., Clarke, W. E., Town, C. D., Nixon, J., Krishnakumar, V., Bidwell, S. L., Denoeud, F., Belcram, H., Links, M. G., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A. S., Pires, C. J., ... Sharpe, A. G. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome biology, 15(6), [R77]. https://doi.org/10.1186/gb-2014-15-6-r77

Vancouver

Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE et al. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome biology. 2014 Jun 10;15(6). R77. https://doi.org/10.1186/gb-2014-15-6-r77

Author

Parkin, Isobel Ap ; 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. / Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. In: Genome biology. 2014 ; Vol. 15, No. 6.

Bibtex - Download

@article{4044c4713f9d41b591db05571d7031bb,
title = "Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea",
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.",
author = "Parkin, {Isobel Ap} and Chushin Koh and Haibao Tang and Robinson, {Stephen J} and Sateesh Kagale and Clarke, {Wayne E} and Town, {Chris D} and John Nixon and Vivek Krishnakumar and Bidwell, {Shelby L} and France Denoeud and Harry Belcram and Links, {Matthew G} and J{\'e}r{\'e}my Just and Carling Clarke and Tricia Bender and Terry Huebert and Mason, {Annaliese S} and Pires, {Chris J} and Guy Barker and Jonathan Moore and Walley, {Peter G} and Sahana Manoli and Jacqueline Batley and Dave Edwards and Nelson, {Matthew N} and Xiyin Wang and Paterson, {Andrew H} and Graham King and Ian Bancroft and Boulos Chalhoub and Sharpe, {Andrew G}",
year = "2014",
month = jun,
day = "10",
doi = "10.1186/gb-2014-15-6-r77",
language = "English",
volume = "15",
journal = "Genome biology",
issn = "1474-760X",
publisher = "BioMed Central",
number = "6",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

AU - Parkin, Isobel Ap

AU - Koh, Chushin

AU - Tang, Haibao

AU - Robinson, Stephen J

AU - Kagale, Sateesh

AU - Clarke, Wayne E

AU - Town, Chris D

AU - Nixon, John

AU - Krishnakumar, Vivek

AU - Bidwell, Shelby L

AU - Denoeud, France

AU - Belcram, Harry

AU - Links, Matthew G

AU - Just, Jérémy

AU - Clarke, Carling

AU - Bender, Tricia

AU - Huebert, Terry

AU - Mason, Annaliese S

AU - Pires, Chris J

AU - Barker, Guy

AU - Moore, Jonathan

AU - Walley, Peter G

AU - Manoli, Sahana

AU - Batley, Jacqueline

AU - Edwards, Dave

AU - Nelson, Matthew N

AU - Wang, Xiyin

AU - Paterson, Andrew H

AU - King, Graham

AU - Bancroft, Ian

AU - Chalhoub, Boulos

AU - Sharpe, Andrew G

PY - 2014/6/10

Y1 - 2014/6/10

N2 - 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.

AB - 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.

U2 - 10.1186/gb-2014-15-6-r77

DO - 10.1186/gb-2014-15-6-r77

M3 - Article

C2 - 24916971

VL - 15

JO - Genome biology

JF - Genome biology

SN - 1474-760X

IS - 6

M1 - R77

ER -