Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster
Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster
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DOI：
10.1073/pnas.0702552104
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发表时间：
2007-07-03
影响因子：
11.1
通讯作者：
Bensasson, Douda
中科院分区：
文献类型：
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作者：
Bergman, Casey M.;Bensasson, Douda
LTR和非LTR反转录转座子在果蝇基因组中表现出不同的丰度模式，但这些差异的原因仍然未知。在这里，我们调查是否LTR和非LTR反转录转座子之间的基因组差异反映了系统的差异，在他们的插入历史。我们发现，对于17个LTR和10个非LTR逆转录转座子家族，它们在类似假基因的进化模式下进化，大多数来自LTR家族的元素在非非洲栖息地的殖民化（大约16，000年前）的最近过去已经整合，而来自非LTR家族的元素自D.黑腹果蝇与其姊妹种拟果蝇（Drosophila simulans）的距离约为5.4 Mya。LTR元件在高重组区和低重组区以及基因区和基因间区中，单独地和按家族地，显著地比非LTR元件年轻。我们表明，分析转座因子（TE）嵌套提供了一种方法来计算转座率从基因组序列，我们估计是一个到两个数量级低于那些基于突变积累的研究。最近的LTR整合提供了一个非平衡的替代低人口频率的LTR元素在这个物种中，一种模式，被经典地解释为证据的选择对转座增加的TE。我们的研究结果要求一类新的群体遗传模型，将TE拷贝数，等位基因频率和插入的年龄，以提供更强大和更强大的推断控制TE在自然群体中的进化的力量。
LTR and non-LTR retrotransposons exhibit distinct patterns of abundance within the Drosophila melanogaster genome, yet the causes of these differences remain unknown. Here we investigate whether genomic differences between LTR and non-LTR retrotransposons reflect systematic differences in their insertion history. We find that for 17 LTR and 10 non-LTR retrotransposon families that evolve under a pseuclogene-like mode of evolution, most elements from LTR families have integrated in the very recent past since colonization of non-African habitats (approximate to 16,000 years ago), whereas elements from non-LTR families have been accumulating in overlapping waves since the divergence of D. melanogaster from its sister species, Drosophila simulans (approximate to 5.4 Mya). LTR elements are significantly younger than non-LTR elements, individually and by family, in regions of high and low recombination, and in genic and intergenic regions. We show that analysis of transposable element (TE) nesting provides a method to calculate transposition rates from genome sequences, which we estimate to be one to two orders of magnitude lowerthan those that are based on mutation accumulation studies. Recent LTR integration provides a nonequilibrium alternative for the low population frequency of LTR elements in this species, a pattern that is classically interpreted as evidence for selection against the transpositional increase of TEs. Our results call for a new class of population genetic models that incorporate TE copy number, allele frequency, and the age of insertions to provide more powerful and robust inferences about the forces that control the evolution of TEs in natural populations.