Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
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DOI：
10.1101/gr.5457707
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发表时间：
2007-02-01
期刊：
影响因子：
7
通讯作者：
Kobayashi, Takehiko
中科院分区：
文献类型：
--
作者：
Ganley, Austen R. D.;Kobayashi, Takehiko
基因组内的重复家族通常保持相似的序列。传统上，这被解释为协同进化，其中阵列中的重复序列通过重组重复序列的持续更替而与相同序列协同进化。另一种形式的进化，出生和死亡的进化，也可以解释这种模式，虽然在这种情况下，选择是维持重复的关键力量。基因组内变异的水平是这两种进化形式之间的关键区别。大重复序列阵列的大小和重复性使得确定基因组内重复序列变异的绝对水平变得困难，因此几乎没有证据支持许多大重复序列阵列的协同进化超过出生和死亡进化。在这里，我们使用全基因组鸟枪序列数据从五种真菌的基因组计划，揭示核糖体RNA基因重复序列（rDNA）内的序列变异的绝对水平。层序变异程度非常低。此外，检测到的多态性在功能上不受限制，似乎存在于选择水平之下。这些结果表明，rDNA是通过协同进化进化。与经历出生和死亡进化的重复序列的比较提供了这两种进化形式之间重复序列变异水平的明显对比，证实了rDNA确实通过协同进化进化而进化。这些低水平的基因组内变异与协同进化的模型一致，其中均质化非常迅速并且有效地维持高度相似的重复序列。
Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve -in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.