Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
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DOI：
10.1101/gr.6070707
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发表时间：
2007-07-01
期刊：
影响因子：
7
通讯作者：
Jurka, Jerzy
中科院分区：
文献类型：
--
作者：
Gentles, Andrew J.;Wakefield, Matthew J.;Jurka, Jerzy
灰色短尾负鼠的基因组以其大尺寸（类似于3.6 Gb）而闻名。我们的特点是近500个家庭的穿插重复的Monodelphis。它们覆盖了基因组的52%，高于迄今为止研究的任何其他羊膜谱系，并可能解释了异常大的基因组大小。与其他哺乳动物相比，Monodelphis显著富含来自LINE-1、CR 1和RTE家族的非LTR反转录转座子，其中> 29%的基因组序列由这些元件的拷贝组成。Monodelphis至少有四个家族的RTE，我们报告支持这种非LTR反转录转座子的水平转移。除了L1动员的短散在元素（西内斯）外，我们还发现了几个似乎使用RTE元素进行动员的西内斯家族。与L1-动员的西内斯相反，在Monodelphis中RTE-动员的西内斯似乎随着时间从G+ C-丰富的区域转移到G+ C-低的区域。内源性逆转录病毒已经占据了负鼠基因组的10%。我们发现，它们的密度是增强的着丝粒和/或端粒区的大多数Monodelphis染色体。我们确定了83个新的古老重复序列家族，这些家族在羊膜谱系中高度保守，包括14个LINE衍生的重复序列;以及一个新的SINE元件MER 131，它可能是一种高度保守的功能性非编码RNA，其出现可以追溯到3亿年前。这些保守重复序列中的许多也存在于人类中，并且在预测的顺式调控模块中高度过量表达。83个家族中有76个存在于鸡和哺乳动物中。
The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size (similar to 3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They cover similar to 52% of the genome, higher than in any other amniotic lineage studied to date, and may account for the unusually large genome size. In comparison to other mammals, Monodelphis is significantly rich in non-LTR retrotransposons from the LINE-1, CR1, and RTE families, with > 29% of the genome sequence comprised of copies of these elements. Monodelphis has at least four families of RTE, and we report support for horizontal transfer of this non-LTR retrotransposon. In addition to short interspersed elements (SINEs) mobilized by L1, we found several families of SINEs that appear to use RTE elements for mobilization. In contrast to L1- mobilized SINEs, the RTE-mobilized SINEs in Monodelphis appear to shift from G+C-rich to G+C-low regions with time. Endogenous retroviruses have colonized similar to 10% of the opossum genome. We found that their density is enhanced in centromeric and/or telomeric regions of most Monodelphis chromosomes. We identified 83 new families of ancient repeats that are highly conserved across amniotic lineages, including 14 LINE-derived repeats; and a novel SINE element, MER131, that may have been exapted as a highly conserved functional noncoding RNA, and whose emergence dates back to similar to 300 million years ago. Many of these conserved repeats are also present in human, and are highly over- represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals.