Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
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DOI：
10.1186/gb-2014-15-6-r77
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发表时间：
2014-06-10
期刊：
影响因子：
12.3
通讯作者：
Sharpe AG
中科院分区：
文献类型：
--
作者：
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 JC;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
甘蓝（Brassica oleracea）是一种有价值的蔬菜物种，数百年来对人类健康和营养做出了贡献，并且包括具有不同形态和植物化学属性的多个不同栽培品种群。除了这种表型财富，B。甘蓝提供了独特的见解多倍体进化，因为它是从多个祖先多倍性事件和最终的甘蓝科特有的三倍体事件的结果。此外，B.甘蓝代表了形成经济上重要的异源多倍体油菜的二倍体基因组之一。对B有了更深的认识。甘蓝基因组结构为整个芸苔属的作物改良策略提供了基础。我们生成一个代表预测B的75%的组件。使用混合Illumina/Roche 454方法对甘蓝基因组进行测序。生成两个密集的遗传图谱，以将几乎92%的组装支架锚到九个假染色体。超过50，000个基因被注释，预计40%的基因组是重复的，从而导致B的基因组大小增加。与它的近亲B相比，拉帕。叶转录组和甲基化组的快照允许在三重亚基因组之间进行比较，这是由最近的拟南芥科特异性多倍体事件引起的。在亚基因组中三重同调序列和胞嘧啶甲基化水平的差异表达表明了导致当前基因组结构的基因组优势的残留标记。虽然胞嘧啶甲基化与单个基因的显性无关，但三重拷贝的独立甲基化模式表明表观遗传机制在重复基因的功能多样化中发挥作用。
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. 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. 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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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
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作者：
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通讯作者：
Osborn, Thomas C.
影响因子：
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Mason, Annaliese S.;Nelson, Matthew N.;Cowling, Wallace A.
通讯作者：
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影响因子：
7
作者：
Lespinet, O;Wolf, YI;Aravind, L
通讯作者：
Aravind, L
影响因子：
11.6
作者：
Cheng, Feng;Mandakova, Terezie;Wang, Xiaowu
通讯作者：
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