Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii.
Rates and Patterns of Mutation in Tandem Repetitive DNA in Six Independent Lineages of Chlamydomonas reinhardtii.
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DOI：
10.1093/gbe/evy123
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发表时间：
2018-07-01
影响因子：
3.3
通讯作者：
Clark AG
中科院分区：
文献类型：
--
作者：
Flynn JM;Lower SE;Barbash DA;Clark AG
短序列重复序列的大串联阵列的突变模式在很大程度上仍然未知，尽管在物种内和物种间观察到它们在序列和基因组丰度上的高水平差异。影响串联重复序列进化动力学的因素很多；然而，它们的进化只在有限的分类群系统发育样本中进行了研究。在这里，我们利用来自6个地理上不同的莱因哈特衣藻分离株的85个单倍体突变积累系的公开全基因组测序数据来研究该物种的串联重复序列的全基因组突变率和模式。我们发现串联重复组成不同的祖先菌株，在全基因组的丰度和存在/不存在的个别重复。估计的突变率（重复拷贝数扩增和收缩）很高，平均每代每单单位拷贝4.3×10−4。尽管这些序列重复突变率比之前报道的其他类型的突变高一个数量级，但比最近在水蚤中发现的低一个数量级，即使在校正了水蚤中较低的全基因组卫星丰度之后也是如此。大多数高丰度重复序列通过单个突变步骤与其他重复序列相关。基因组内重复拷贝数变化的相关性揭示了密切相关的重复序列簇，它们呈正相关或负相关，并且在两个不同的突变积累实验中独立出现了类似的相关模式。总之，这些结果描绘了这种单细胞藻类串联重复进化的动态画面。
The mutational patterns of large tandem arrays of short sequence repeats remain largely unknown, despite observations of their high levels of variation in sequence and genomic abundance within and between species. Many factors can influence the dynamics of tandem repeat evolution; however, their evolution has only been examined over a limited phylogenetic sample of taxa. Here, we use publicly available whole-genome sequencing data of 85 haploid mutation accumulation lines derived from six geographically diverse Chlamydomonas reinhardtii isolates to investigate genome-wide mutation rates and patterns in tandem repeats in this species. We find that tandem repeat composition differs among ancestral strains, both in genome-wide abundance and presence/absence of individual repeats. Estimated mutation rates (repeat copy number expansion and contraction) were high, averaging 4.3×10−4 per generation per single unit copy. Although orders of magnitude higher than other types of mutation previously reported in C. reinhardtii, these tandem repeat mutation rates were one order of magnitude lower than what has recently been found in Daphnia pulex, even after correcting for lower overall genome-wide satellite abundance in C. reinhardtii. Most high-abundance repeats were related to others by a single mutational step. Correlations of repeat copy number changes within genomes revealed clusters of closely related repeats that were strongly correlated positively or negatively, and similar patterns of correlation arose independently in two different mutation accumulation experiments. Together, these results paint a dynamic picture of tandem repeat evolution in this unicellular alga.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.5
作者：
Langley SA;Karpen GH;Langley CH
通讯作者：
Langley CH
影响因子：
7
作者：
Keith N;Tucker AE;Jackson CE;Sung W;Lucas Lledó JI;Schrider DR;Schaack S;Dudycha JL;Ackerman M;Younge AJ;Shaw JR;Lynch M
通讯作者：
Lynch M
影响因子：
56.9
作者：
Hoskins, Roger A.;Carlson, Joseph W.;Celniker, Susan E.
通讯作者：
Celniker, Susan E.
影响因子：
56.9
作者：
Lynch, M;Conery, JS
通讯作者：
Conery, JS