Organization and evolution of transposable elements along the bread wheat chromosome 3B.
Organization and evolution of transposable elements along the bread wheat chromosome 3B.
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DOI：
10.1186/s13059-014-0546-4
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发表时间：
2014
期刊：
影响因子：
12.3
通讯作者：
Choulet F
中科院分区：
文献类型：
--
作者：
Daron J;Glover N;Pingault L;Theil S;Jamilloux V;Paux E;Barbe V;Mangenot S;Alberti A;Wincker P;Quesneville H;Feuillet C;Choulet F
17 Gb面包小麦基因组通过转座因子（TE）的增殖和最近两轮的多倍化而大规模扩增。小麦3B染色体774 Mb参考序列的组装为我们提供了一个机会，以迄今为止尚未达到的分辨率和规模探索TE对复杂小麦基因组结构和进化的影响。我们开发了一个自动化的工作流程，TERI-TE，在复杂的基因组TE建模。我们沿着3B假分子精确地描绘了56，488个完整的和196，391个片段化的TE，占序列的85%，并重建了30，199个嵌套插入。在过去的100万年里，TE大多是沉默的，3B染色体是由100万到300万年前发生的一系列爆发形成的。加速TE消除在高重组远端区域是一个驱动力染色体分区。在高重组远端区域中过度表达的CACTA与最近复制的基因显著相关。此外，我们确定了140个CACTA介导的基因捕获事件，其中17个基因可能通过外显子改组产生，并显示19个捕获的基因被转录和选择压力下，这表明CACTA在最近的小麦适应中的重要作用。精确的TE建模揭示了高度复杂的多倍体基因组中TE的动态。它为染色体分配提供了新的见解，并强调了CACTA转座子在小麦高水平基因复制中的作用。本文的在线版本（doi：10.1186/s13059-014-0546-4）包含补充材料，可供授权用户使用。
The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation. Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat. The online version of this article (doi:10.1186/s13059-014-0546-4) contains supplementary material, which is available to authorized users.
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影响因子：
5.4
作者：
Chatterjee, Atreyi Ghatak;Leem, Young Eun;Levin, Henry L.
通讯作者：
Levin, Henry L.
影响因子：
4.4
作者：
Han Y;Qin S;Wessler SR
通讯作者：
Wessler SR
影响因子：
4.5
作者：
Baucom RS;Estill JC;Chaparro C;Upshaw N;Jogi A;Deragon JM;Westerman RP;Sanmiguel PJ;Bennetzen JL
通讯作者：
Bennetzen JL
影响因子：
56.9
作者：
Choulet, Frederic;Alberti, Adriana;Feuillet, Catherine
通讯作者：
Feuillet, Catherine
影响因子：
3.3
作者：
El Baidouri M;Panaud O
通讯作者：
Panaud O