MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals.
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals.
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DOI：
10.1093/gbe/evw029
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发表时间：
2016-02-12
影响因子：
3.3
通讯作者：
Okada N
中科院分区：
文献类型：
--
作者：
Nishihara H;Plazzi F;Passamonti M;Okada N
西内斯（短散布元件）是转座元件，通常独立起源于每个分类学分支（目/科）。然而，一些SINE家族共享高度相似的中心序列，因此被归类为SINE超家族。尽管目前只报道了4个SINE超家族（CORE-SINE、V-SINE、DeuSINE和Ceph-SINE），但通过对后生动物基因组中新西内斯的深入研究，有望发现新的SINE超家族。在这里，我们描述了15个西内斯，其中13个是新的，有一个类似的66 bp的中心区域，因此构成了一个新的SINE超家族，MetaSINE。从鱼类到刺胞动物都有分布，表明它们的共同进化起源至少为640 Ma。由于MetaSINEs的3′尾是可变的，这些西内斯很可能在进化过程中通过改变其伴侣长散布元件进行逆转录转座而存活下来。此外，我们研究了双壳类基因组中其他SINE超家族成员的存在，并表征了8个新的西内斯，它们属于核心SINE、V-SINE和DeuSINE，以及MetaSINE。双壳类西内斯的广泛分布表明，至少有三个西内斯起源于双壳类的共同祖先。我们的比较分析的中心域的西内斯显示，在每个超家族，只有一个限制区域是共享的所有成员。由于SINE超家族的中心结构域的功能仍然是未知的，这样的结构信息的SINE超家族将是有用的，为未来的实验和比较分析，以揭示为什么他们一直保留在后生动物的基因组在进化过程中。
SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3′ tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution.