Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.
Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.
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DOI：
10.1093/gbe/evt025
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发表时间：
2013
影响因子：
3.3
通讯作者：
Panaud O
中科院分区：
文献类型：
--
作者：
El Baidouri M;Panaud O
长末端重复-反转录转座子(LTR-RTS)是植物中含量最丰富的一类转座元件。它们强烈影响宿主基因组的结构、功能和进化，特别是它们在基因组大小变化中的作用已经明确。然而，由于缺乏比较研究，LTR-RTS具有不同形状的植物基因组的过程的动力学仍然知之甚少。使用一种新的稳健和自动化的家族分类方法，我们在8个有高质量序列可用的植物基因组中详尽地描述了LTR-RTS(即，拟南芥、甘蓝、葡萄、大豆、水稻、Brachypodium dystachion、高粱和玉米)。这使得我们能够对这八个单子叶和双子叶植物谱系中的逆转位景观进行全基因组的比较研究。我们发现，逆转录转座在所有被研究的植物基因组中反复发生，无论其大小如何，并且是通过猝发发生的，而不是一个连续的过程。此外，在每个基因组中，只有一个或几个LTR-RT家族在最近的过去是活跃的，因此所研究物种之间的基因组大小的差异可以主要由最近的易位爆发的程度来解释(S)。在这些爆发之后，LTR-RTS通过重组和缺失从宿主基因组中有效地消除，但我们表明移除速度不是谱系特有的。这些新的发现使我们提出了一个由TE驱动的植物基因组进化的新模型。
Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.
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影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
影响因子：
64.8
作者：
Ito, Hidetaka;Gaubert, Herve;Paszkowski, Jerzy
通讯作者：
Paszkowski, Jerzy
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
7
作者：
Ma, JX;Devos, KM;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
5.8
作者：
McCarthy, EM;McDonald, JF
通讯作者：
McDonald, JF