Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
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 uni...
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| Autor*in: |
Parkin, Isobel AP [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2014 |
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| Anmerkung: |
© Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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| Übergeordnetes Werk: |
Enthalten in: Genome biology - London : BioMed Central, 2000, 15(2014), 6 vom: 10. Juni |
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| Übergeordnetes Werk: |
volume:15 ; year:2014 ; number:6 ; day:10 ; month:06 |
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| DOI / URN: |
10.1186/gb-2014-15-6-r77 |
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| Katalog-ID: |
SPR030021006 |
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| 245 | 1 | 0 | |a Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea |
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| 520 | |a 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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| 650 | 4 | |a Gene Body Methylation |7 (dpeaa)DE-He213 | |
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| 700 | 1 | |a Koh, Chushin |4 aut | |
| 700 | 1 | |a Tang, Haibao |4 aut | |
| 700 | 1 | |a Robinson, Stephen J |4 aut | |
| 700 | 1 | |a Kagale, Sateesh |4 aut | |
| 700 | 1 | |a Clarke, Wayne E |4 aut | |
| 700 | 1 | |a Town, Chris D |4 aut | |
| 700 | 1 | |a Nixon, John |4 aut | |
| 700 | 1 | |a Krishnakumar, Vivek |4 aut | |
| 700 | 1 | |a Bidwell, Shelby L |4 aut | |
| 700 | 1 | |a Denoeud, France |4 aut | |
| 700 | 1 | |a Belcram, Harry |4 aut | |
| 700 | 1 | |a Links, Matthew G |4 aut | |
| 700 | 1 | |a Just, Jérémy |4 aut | |
| 700 | 1 | |a Clarke, Carling |4 aut | |
| 700 | 1 | |a Bender, Tricia |4 aut | |
| 700 | 1 | |a Huebert, Terry |4 aut | |
| 700 | 1 | |a Mason, Annaliese S |4 aut | |
| 700 | 1 | |a Pires, J Chris |4 aut | |
| 700 | 1 | |a Barker, Guy |4 aut | |
| 700 | 1 | |a Moore, Jonathan |4 aut | |
| 700 | 1 | |a Walley, Peter G |4 aut | |
| 700 | 1 | |a Manoli, Sahana |4 aut | |
| 700 | 1 | |a Batley, Jacqueline |4 aut | |
| 700 | 1 | |a Edwards, David |4 aut | |
| 700 | 1 | |a Nelson, Matthew N |4 aut | |
| 700 | 1 | |a Wang, Xiyin |4 aut | |
| 700 | 1 | |a Paterson, Andrew H |4 aut | |
| 700 | 1 | |a King, Graham |4 aut | |
| 700 | 1 | |a Bancroft, Ian |4 aut | |
| 700 | 1 | |a Chalhoub, Boulos |4 aut | |
| 700 | 1 | |a Sharpe, Andrew G |4 aut | |
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10.1186/gb-2014-15-6-r77 doi (DE-627)SPR030021006 (SPR)gb-2014-15-6-r77-e DE-627 ger DE-627 rakwb eng Parkin, Isobel AP verfasserin aut Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( 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. Cytosine Methylation (dpeaa)DE-He213 Whole Genome Duplication (dpeaa)DE-He213 Whole Genome Duplication Event (dpeaa)DE-He213 Gene Body Methylation (dpeaa)DE-He213 Single Base Resolution (dpeaa)DE-He213 Koh, Chushin aut Tang, Haibao aut Robinson, Stephen J aut Kagale, Sateesh aut Clarke, Wayne E aut Town, Chris D aut Nixon, John aut Krishnakumar, Vivek aut Bidwell, Shelby L aut Denoeud, France aut Belcram, Harry aut Links, Matthew G aut Just, Jérémy aut Clarke, Carling aut Bender, Tricia aut Huebert, Terry aut Mason, Annaliese S aut Pires, J Chris aut Barker, Guy aut Moore, Jonathan aut Walley, Peter G aut Manoli, Sahana aut Batley, Jacqueline aut Edwards, David aut Nelson, Matthew N aut Wang, Xiyin aut Paterson, Andrew H aut King, Graham aut Bancroft, Ian aut Chalhoub, Boulos aut Sharpe, Andrew G aut Enthalten in Genome biology London : BioMed Central, 2000 15(2014), 6 vom: 10. Juni (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:15 year:2014 number:6 day:10 month:06 https://dx.doi.org/10.1186/gb-2014-15-6-r77 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2014 6 10 06 |
| spelling |
10.1186/gb-2014-15-6-r77 doi (DE-627)SPR030021006 (SPR)gb-2014-15-6-r77-e DE-627 ger DE-627 rakwb eng Parkin, Isobel AP verfasserin aut Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( 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. Cytosine Methylation (dpeaa)DE-He213 Whole Genome Duplication (dpeaa)DE-He213 Whole Genome Duplication Event (dpeaa)DE-He213 Gene Body Methylation (dpeaa)DE-He213 Single Base Resolution (dpeaa)DE-He213 Koh, Chushin aut Tang, Haibao aut Robinson, Stephen J aut Kagale, Sateesh aut Clarke, Wayne E aut Town, Chris D aut Nixon, John aut Krishnakumar, Vivek aut Bidwell, Shelby L aut Denoeud, France aut Belcram, Harry aut Links, Matthew G aut Just, Jérémy aut Clarke, Carling aut Bender, Tricia aut Huebert, Terry aut Mason, Annaliese S aut Pires, J Chris aut Barker, Guy aut Moore, Jonathan aut Walley, Peter G aut Manoli, Sahana aut Batley, Jacqueline aut Edwards, David aut Nelson, Matthew N aut Wang, Xiyin aut Paterson, Andrew H aut King, Graham aut Bancroft, Ian aut Chalhoub, Boulos aut Sharpe, Andrew G aut Enthalten in Genome biology London : BioMed Central, 2000 15(2014), 6 vom: 10. Juni (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:15 year:2014 number:6 day:10 month:06 https://dx.doi.org/10.1186/gb-2014-15-6-r77 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2014 6 10 06 |
| allfields_unstemmed |
10.1186/gb-2014-15-6-r77 doi (DE-627)SPR030021006 (SPR)gb-2014-15-6-r77-e DE-627 ger DE-627 rakwb eng Parkin, Isobel AP verfasserin aut Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( 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. Cytosine Methylation (dpeaa)DE-He213 Whole Genome Duplication (dpeaa)DE-He213 Whole Genome Duplication Event (dpeaa)DE-He213 Gene Body Methylation (dpeaa)DE-He213 Single Base Resolution (dpeaa)DE-He213 Koh, Chushin aut Tang, Haibao aut Robinson, Stephen J aut Kagale, Sateesh aut Clarke, Wayne E aut Town, Chris D aut Nixon, John aut Krishnakumar, Vivek aut Bidwell, Shelby L aut Denoeud, France aut Belcram, Harry aut Links, Matthew G aut Just, Jérémy aut Clarke, Carling aut Bender, Tricia aut Huebert, Terry aut Mason, Annaliese S aut Pires, J Chris aut Barker, Guy aut Moore, Jonathan aut Walley, Peter G aut Manoli, Sahana aut Batley, Jacqueline aut Edwards, David aut Nelson, Matthew N aut Wang, Xiyin aut Paterson, Andrew H aut King, Graham aut Bancroft, Ian aut Chalhoub, Boulos aut Sharpe, Andrew G aut Enthalten in Genome biology London : BioMed Central, 2000 15(2014), 6 vom: 10. Juni (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:15 year:2014 number:6 day:10 month:06 https://dx.doi.org/10.1186/gb-2014-15-6-r77 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2014 6 10 06 |
| allfieldsGer |
10.1186/gb-2014-15-6-r77 doi (DE-627)SPR030021006 (SPR)gb-2014-15-6-r77-e DE-627 ger DE-627 rakwb eng Parkin, Isobel AP verfasserin aut Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( 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. Cytosine Methylation (dpeaa)DE-He213 Whole Genome Duplication (dpeaa)DE-He213 Whole Genome Duplication Event (dpeaa)DE-He213 Gene Body Methylation (dpeaa)DE-He213 Single Base Resolution (dpeaa)DE-He213 Koh, Chushin aut Tang, Haibao aut Robinson, Stephen J aut Kagale, Sateesh aut Clarke, Wayne E aut Town, Chris D aut Nixon, John aut Krishnakumar, Vivek aut Bidwell, Shelby L aut Denoeud, France aut Belcram, Harry aut Links, Matthew G aut Just, Jérémy aut Clarke, Carling aut Bender, Tricia aut Huebert, Terry aut Mason, Annaliese S aut Pires, J Chris aut Barker, Guy aut Moore, Jonathan aut Walley, Peter G aut Manoli, Sahana aut Batley, Jacqueline aut Edwards, David aut Nelson, Matthew N aut Wang, Xiyin aut Paterson, Andrew H aut King, Graham aut Bancroft, Ian aut Chalhoub, Boulos aut Sharpe, Andrew G aut Enthalten in Genome biology London : BioMed Central, 2000 15(2014), 6 vom: 10. Juni (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:15 year:2014 number:6 day:10 month:06 https://dx.doi.org/10.1186/gb-2014-15-6-r77 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2014 6 10 06 |
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10.1186/gb-2014-15-6-r77 doi (DE-627)SPR030021006 (SPR)gb-2014-15-6-r77-e DE-627 ger DE-627 rakwb eng Parkin, Isobel AP verfasserin aut Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( 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. Cytosine Methylation (dpeaa)DE-He213 Whole Genome Duplication (dpeaa)DE-He213 Whole Genome Duplication Event (dpeaa)DE-He213 Gene Body Methylation (dpeaa)DE-He213 Single Base Resolution (dpeaa)DE-He213 Koh, Chushin aut Tang, Haibao aut Robinson, Stephen J aut Kagale, Sateesh aut Clarke, Wayne E aut Town, Chris D aut Nixon, John aut Krishnakumar, Vivek aut Bidwell, Shelby L aut Denoeud, France aut Belcram, Harry aut Links, Matthew G aut Just, Jérémy aut Clarke, Carling aut Bender, Tricia aut Huebert, Terry aut Mason, Annaliese S aut Pires, J Chris aut Barker, Guy aut Moore, Jonathan aut Walley, Peter G aut Manoli, Sahana aut Batley, Jacqueline aut Edwards, David aut Nelson, Matthew N aut Wang, Xiyin aut Paterson, Andrew H aut King, Graham aut Bancroft, Ian aut Chalhoub, Boulos aut Sharpe, Andrew G aut Enthalten in Genome biology London : BioMed Central, 2000 15(2014), 6 vom: 10. Juni (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:15 year:2014 number:6 day:10 month:06 https://dx.doi.org/10.1186/gb-2014-15-6-r77 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 15 2014 6 10 06 |
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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, J Chris Barker, Guy Moore, Jonathan Walley, Peter G Manoli, Sahana Batley, Jacqueline Edwards, David Nelson, Matthew N Wang, Xiyin Paterson, Andrew H King, Graham Bancroft, Ian Chalhoub, Boulos Sharpe, Andrew G |
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transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid brassica oleracea |
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Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea |
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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. © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstractGer |
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. © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstract_unstemmed |
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. © Parkin et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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