The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis.
The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis.
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DOI：
10.1016/j.gene.2008.11.030
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发表时间：
2009-07
期刊：
影响因子：
3.5
通讯作者：
O. Piskurek;Hidenori Nishihara;N. Okada
中科院分区：
文献类型：
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作者：
O. Piskurek;Hidenori Nishihara;N. Okada
转座因子已在许多脊椎动物，包括哺乳动物，鸟类和鱼类的全基因组中得到表征。安诺利斯卡罗莱纳州草案大会提供了第一个机会，研究逆转录酶在爬行动物基因组。在这里，我们根据数据库搜索鉴定并重建了许多逆转录酶：五个蜥类短散布元件（SINE）亚家族、5S-Sauria SINE嵌合体、Anolis Bov-B长散布元件（LINE）、Anolis SINE 2、Anolis LINE 2、Anolis LINE 1、Anolis CR 1和含有染色体结构域的Ty 3/Gypsy LTR元件。我们专注于两个SINE系列（Anolis Sauria SINE和Anolis SINE 2）及其合作伙伴LINE系列（Anolis Bov-B LINE和Anolis LINE 2）。我们证明了每个SINE/LINE对的分布相似，并预测进化上较年轻的SINE成员的逆转录转座是通过较年轻的Bov-B LINE成员进行的，而在它们各自的进化上较年长的SINE/LINE成员之间也存在核心化。进化上最年轻的蜥类SINE序列进化为新型滚环转座子的一部分。当Bov-B LINES和Sauria西内斯在其反转录转座中不太活跃时的进化时间框架的特征在于Anolis SINE 2和Anolis LINE 2元件的高反转录转座爆发。我们还表征了第一个全长的色病毒LTR元件在Escherotes（Amn-ichi）。这种新发现的染色体病毒在阿诺利斯基因组中广泛存在，并且保存得非常好，表明它仍然活跃。安氏基因组中的转座因子约占总DNA序列的20%，而这一比例是许多哺乳动物基因组中转座因子的两倍多，其中这些转座因子具有重要的生物学功能。然而，20%的转座因子覆盖率足以预测Anolis反转录子和其他移动的因子也可能具有生物学和进化相关的功能。Anolis基因组中新的西内斯和LINES以及其他普遍存在的基因组元件将被证明对比较基因组学、遗传学和功能遗传学的研究非常有用。
Transposable elements have been characterized in a number of vertebrates, including whole genomes of mammals, birds, and fishes. The Anolis carolinensis draft assembly provides the first opportunity to study retroposons in a reptilian genome. Here, we identified and reconstructed a number of retroposons based on database searches: Five Sauria short interspersed element (SINE) subfamilies, 5S-Sauria SINE chimeras, Anolis Bov-B long interspersed element (LINE), Anolis SINE 2, Anolis LINE 2, Anolis LINE 1, Anolis CR 1, and a chromodomain-containing Ty3/Gypsy LTR element. We focused on two SINE families (Anolis Sauria SINE and Anolis SINE 2) and their partner LINE families (Anolis Bov-B LINE and Anolis LINE 2). We demonstrate that each SINE/LINE pair is distributed similarly and predict that the retrotransposition of evolutionarily younger Sauria SINE members is via younger Bov-B LINE members while a corellation also exists between their respective evolutionarily older SINE/LINE members. The evolutionarily youngest Sauria SINE sequences evolved as part of novel rolling-circle transposons. The evolutionary time frame when Bov-B LINEs and Sauria SINEs were less active in their retrotransposition is characterized by a high retrotransposition burst of Anolis SINE 2 and Anolis LINE 2 elements. We also characterized the first full-length chromoviral LTR element in amniotes (Amn-ichi). This newly identified chromovirus is widespread in the Anolis genome and has been very well preserved, indicating that it is still active. Transposable elements in the Anolis genome account for approximately 20% of the total DNA sequence, whereas the proportion is more than double that in many mammalian genomes in which such elements have important biological functions. Nevertheless, 20% transposable element coverage is sufficient to predict that Anolis retroposons and other mobile elements also may have biologically and evolutionarily relevant functions. The new SINEs and LINEs and other ubiquitous genomic elements characterized in the Anolis genome will prove very useful for studies in comparative genomics, phylogenetics, and functional genetics.