Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
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DOI：
10.1101/gr.074187.107
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发表时间：
2008-07-01
期刊：
影响因子：
7
通讯作者：
Nielsen, Rasmus
中科院分区：
文献类型：
--
作者：
Hellmann, Ines;Mang, Yuan;Nielsen, Rasmus
我们介绍了一个简单的，广泛适用的方法，从基因组鸟枪测序数据获得核苷酸多样性θ的估计。该方法考虑了这些数据的特殊性质：从一个或多个个体中随机取样基因组片段，以及个体读数的相对较高的错误率。应用这种方法从塞雷拉人类基因组测序和SNP发现项目的数据，我们获得的估计核苷酸多样性的窗口跨越人类基因组，并显示多样性的分歧比降低低重组的区域。此外，我们发现端粒区域的多样性升高主要是由于突变率升高，而不是由于背景选择水平降低。然而，我们发现的迹象表明，端粒以及着丝粒经历更大的影响，自然选择比染色体内区域。最后，我们确定了一些基因组区域的增加或减少的多样性相比，当地水平的人类-黑猩猩的分歧和本地重组率。
We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity theta from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show that the elevated diversity in telomeric regions is mainly due to elevated mutation rates and not due to decreased levels of background selection. However, we find indications that telomeres as well as centromeres experience greater impact from natural selection than intrachromosomal regions. Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate.