Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex
Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex
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DOI：
10.1534/genetics.117.300146
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发表时间：
2017-10-01
期刊：
影响因子：
3.3
通讯作者：
Clark, Andrew G.
中科院分区：
文献类型：
--
作者：
Flynn, Jullien M.;Caldas, Ian;Clark, Andrew G.
一个长期存在的进化难题是，所有真核生物的基因组都含有大量串联重复的DNA，即使在密切相关的物种之间，其序列基序和丰度也有很大差异。为了阐明串联重复动力学的进化力量，重复拷贝数的突变率和模式的量化及其选择性中性测试是必要的。在这里，我们使用的全基因组序列的28突变积累（MA）线蚤状蚤，除了6个菌株从一个非MA人口起源于同一祖先，既估计突变率的重复序列丰度和评估的选择性制度对他们的作用。我们发现，单个重复序列的突变率都很高，高度可变，范围从添加/删除0.29-105拷贝每一代（反映每代0.120.80%的变化）。我们的研究结果还提供了证据表明，新的重复序列往往是从现有的。非MA群体分离株显示出纯化或稳定选择的信号，平均比MA系的重复拷贝数变异低33%，尽管选择性约束水平在所有重复中不是均匀分布的。多对重复序列之间的变化具有相关性，且MA系与非MA群体之间的相关模式存在显著差异。我们的研究表明，串联重复序列在拷贝数上可以经历极其快速的进化，这可能导致密切相关的物种之间全基因组重复序列组成的高度分化。
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here, we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex, in addition to six isolates from a non-MA population originating from the same progenitor, to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual repeats were both high and highly variable, ranging from additions/deletions of 0.29-105 copies per generation ( reflecting changes of 0.120.80% per generation). Our results also provide evidence that new repeat sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33% lower variation in repeat copy number on average than the MA lines, although the level of selective constraint was not evenly distributed across all repeats. The changes between many pairs of repeats were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that tandem repeats can experience extremely rapid evolution in copy number, which can lead to high levels of divergence in genome-wide repeat composition between closely related species.