Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome.
Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome.
复制标题
DOI：
10.1093/gbe/evs046
复制
发表时间：
2012
影响因子：
3.3
通讯作者：
Tiffin P
中科院分区：
文献类型：
--
作者：
Paape T;Zhou P;Branca A;Briskine R;Young N;Tiffin P
在许多物种中，突变率在基因组中各不相同，与几个基因组特征有显著关系，包括到着丝粒的距离、基因密度和GC含量。对精细尺度重组率的研究还表明，在几个物种中，存在重组热点，即重组率比周围区域高10-100倍的短区域。在这项研究中，我们分析了全基因组重测序数据从26个加入模式豆科苜蓿蒺藜深入了解基因组特征，相关的高和低重组率和重组热点在1 kb的规模。我们发现，所有三条染色体上的高重组区域（1-kb窗口中的最高5%的分布）显着更接近着丝粒，有更高的基因密度，和较低的GC含量比低重组窗口。高重组窗口在一些基因功能类别中也显著过高，最强烈的是NB-ARC和LRR基因，这两个基因在植物防御病原体中都很重要。类似于高重组窗口，重组热点（1 kb的窗口，具有显着更高的重组比周围地区）显着更接近着丝粒比非热点窗口。相比之下，我们检测到热点和非热点窗口之间的基因密度或GC含量没有差异。使用线性模型小波分析来研究重组和基因组特征之间的关系，在多个空间尺度上，我们发现一个显着的负相关性与距离着丝粒跨越尺度高达512 kb，而基因密度和GC含量显示显着的正相关和负相关，分别只有64 kb。重组和基因组特征之间的相关性，特别是基因密度和多态性，表明它们是规模依赖性的，需要在与这些特征的演变相关的规模上进行评估。
Recombination rates vary across the genome and in many species show significant relationships with several genomic features, including distance to the centromere, gene density, and GC content. Studies of fine-scale recombination rates have also revealed that in several species, there are recombination hotspots, that is, short regions with recombination rates 10–100 greater than those in surrounding regions. In this study, we analyzed whole-genome resequence data from 26 accessions of the model legume Medicago truncatula to gain insight into the genomic features that are related to high- and low-recombination rates and recombination hotspots at 1 kb scales. We found that high-recombination regions (1-kb windows among those in the highest 5% of the distribution) on all three chromosomes were significantly closer to the centromere, had higher gene density, and lower GC content than low-recombination windows. High-recombination windows are also significantly overrepresented among some gene functional categories—most strongly NB–ARC and LRR genes, both of which are important in plant defense against pathogens. Similar to high-recombination windows, recombination hotspots (1-kb windows with significantly higher recombination than the surrounding region) are significantly nearer to the centromere than nonhotspot windows. By contrast, we detected no difference in gene density or GC content between hotspot and nonhotspot windows. Using linear model wavelet analysis to examine the relationship between recombination and genomic features across multiple spatial scales, we find a significant negative correlation with distance to the centromere across scales up to 512 kb, whereas gene density and GC content show significantly positive and negative correlations, respectively, only up to 64 kb. Correlations between recombination and genomic features, particularly gene density and polymorphism, suggest that they are scale dependent and need to be assessed at scales relevant to the evolution of those features.
登录
查看更多内容
影响因子：
7
作者：
Anderson, LK;Lai, A;Gaut, BS
通讯作者：
Gaut, BS
影响因子：
5.8
作者：
Fearnhead, Paul
通讯作者：
Fearnhead, Paul
影响因子：
30.8
作者：
Jeffreys, AJ;Kauppi, L;Neumann, R
通讯作者：
Neumann, R
DOI：
10.1111/1467-9868.00355
发表时间：
2002-01-01
影响因子：
5.8
作者：
Fearnhead, P;Donnelly, P
通讯作者：
Donnelly, P
影响因子：
30.8
作者：
Horton, Matthew W.;Hancock, Angela M.;Huang, Yu S.;Toomajian, Christopher;Atwell, Susanna;Auton, Adam;Muliyati, N. Wayan;Platt, Alexander;Sperone, F. Gianluca;Vilhjalmsson, Bjarni J.;Nordborg, Magnus;Borevitz, Justin O.;Bergelson, Joy
通讯作者：
Bergelson, Joy