Short interspersed elements (SINEs) in plants: Origin, classification, and use as phylogenetic markers
Short interspersed elements (SINEs) in plants: Origin, classification, and use as phylogenetic markers
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DOI：
10.1080/10635150601047843
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发表时间：
2006-12-01
影响因子：
6.5
通讯作者：
Zhang, Xiaoyu
中科院分区：
文献类型：
--
作者：
Deragon, Jean-Marc;Zhang, Xiaoyu
短散布元件 (SINES) 是一类分散的移动序列，它使用 RNA 作为称为逆转录的扩增过程中的中间体。给定基因座上是否存在 SINE 已被用作评估物种之间系统发育关系的有意义的分类标准。我们在此回顾植物 SINE 表征的最新进展以及它们作为分子制造者的用途，以追溯野生和栽培的稻和芸苔属物种之间的系统发育关系。在十字花科中，由于我们对内源 SINE 家族（其起源和进化历史）的部分了解以及缺乏明确的分类，SINE 标记的进一步使用受到限制。为了解决这个问题，我们分析了所有已知十字花科 SINE 之间的系统发育关系，并提出了一种新的分类，将 SINE 分为 15 个不同的科。评估了每个十字花科 SINE 家族的相对年龄和大小，并描述了新的系统发育支持的亚科。我们还提供的证据表明，最近在甘蓝中通过对先前存在的 SINE 部分的改组而出现了新的潜在活性 SINE。最后，拟南芥和甘蓝中存在的 SINE fan-Lilies 的比较进化历史表明，SINES 在芸苔属谱系中总体上更为活跃。讨论了这些新数据对于在未来应用中使用十字花科 SINES 作为分子标记的重要性。
Short interspersed elements (SINES) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE fan-Lilies present in Arabidopsis thaliana and Brassica oleracea revealed that SINES were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINES as molecular markers in future applications is discussed.