Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.
Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.
复制标题
DOI：
10.1101/gr.215095.116
复制
发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Wolf JBW
中科院分区：
文献类型：
--
作者：
Weissensteiner MH;Pang AWC;Bunikis I;Höijer I;Vinnere-Petterson O;Suh A;Wolf JBW
准确和连续的基因组组装是全面理解形成基因组多样性和进化的过程的关键。然而，它经常受到结构性异染色质的限制，通常以高度重复的DNA为特征。作为与着丝粒和亚端粒区域相关的基因组结构的关键特征，它在局部影响减数分裂重组。在这项研究中，我们评估了大型串联重复序列对鸟类物种形成模型欧亚乌鸦重组率图景的影响。我们使用单分子实时测序(长读组装[LR])和单分子光学图谱(光学图谱组装[OM])组装了两个高质量的基因组参考。包括为同一个人构建的已发布短读程序集(SR)的三向比较允许评估程序集特性并精确定位错误程序集。通过结合来自所有三个组装的信息，我们描述了在序列组装断点附近的36个以前未识别的大重复区域，其中大部分包含14kb卫星重复或其1.2kb亚单位的复杂阵列。使用全基因组种群重测序数据，我们估计了种群规模重组率(ρ)，并发现在这些地区它显著降低。这些发现与着丝粒或亚端粒异染色质邻近区域的低重组效应是一致的，并增加了我们对在基因组上产生遗传多样性和分化的广泛异质性的过程的理解。通过结合三种不同的技术，我们的结果强调了增加一层关于基因组结构的信息的重要性，这是每种方法都无法独立获取的。
Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.