Mouse segmental duplication and copy number variation
Mouse segmental duplication and copy number variation
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DOI：
10.1038/ng.172
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发表时间：
2008-07-01
期刊：
影响因子：
30.8
通讯作者：
Eichler, Evan E.
中科院分区：
文献类型：
--
作者：
She, Xinwei;Cheng, Ze;Eichler, Evan E.
对基于克隆的基因组组装的详细分析表明，与之前全基因组霰弹枪序列组装的估计相比，小鼠最近的重复含量（4.94%）现在与人类（5.5%）相当。然而，小鼠和人类基因组的结构明显不同：大多数小鼠的重复被组织成离散的串联重复簇，显示基因和转录本的消耗和长穿插核元件（LINE）和长末端重复（LTR）反转录子的富集。我们评估了之前用于遗传关联研究、测序和小鼠表型计划的15个小鼠品系中C57BL/6J重复区域的拷贝数变化。我们确定超过60%的这些碱基对在菌株之间是多态的（平均而言，不同小鼠菌株之间有20 Mb的拷贝数可变DNA）。我们的数据表明，与人类相比，不同的小鼠品系表现出相当的拷贝数多态性，如果不是更大的话；然而，这种变化更多地受到局部限制。我们展示了与精子发生、妊娠、胎生、信息素信号和免疫反应相关的大基因家族的大而复杂的株系间拷贝数变异模式。
Detailed analyses of the clone-based genome assembly reveal that the recent duplication content of mouse (4.94%) is now comparable to that of human (5.5%), in contrast to previous estimates from the whole-genome shotgun sequence assembly. However, the architecture of mouse and human genomes differs markedly: most mouse duplications are organized into discrete clusters of tandem duplications that show depletion of genes and transcripts and enrichment of long interspersed nuclear element (LINE) and long terminal repeat (LTR) retroposons. We assessed copy number variation of the C57BL/6J duplicated regions within 15 mouse strains previously used for genetic association studies, sequencing and the Mouse Phenome Project. We determined that over 60% of these base pairs are polymorphic among the strains (on average, there was 20 Mb of copy-number-variable DNA between different mouse strains). Our data suggest that different mouse strains show comparable, if not greater, copy number polymorphism when compared to human; however, such variation is more locally restricted. We show large and complex patterns of interstrain copy number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and immune response.