Department of Plant Biology, University of Minnesota, MN, USA.
Genome Biol Evol. 2012;4(5):726-37. doi: 10.1093/gbe/evs046. Epub 2012 May 3.
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.
重组率在基因组中存在差异，在许多物种中与多个基因组特征存在显著关系，包括与着丝粒的距离、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出 10-100 倍的短区域。在这项研究中，我们分析了模式豆科植物蒺藜苜蓿 26 个品系的全基因组重测序数据，以深入了解与 1kb 尺度上高重组率和低重组率以及重组热点相关的基因组特征。我们发现，在所有三个染色体上，高重组率区域（在分布的前 5%的 1kb 窗口中）都显著更接近着丝粒，基因密度更高，GC 含量更低。高重组率窗口在一些基因功能类别中也有显著的过表达，尤其是 NB-ARC 和 LRR 基因，它们在植物抵御病原体的防御中都很重要。与高重组率窗口相似，重组热点（比周围区域显著更高重组率的 1kb 窗口）比非热点窗口更接近着丝粒。相比之下，我们没有发现热点窗口和非热点窗口之间在基因密度或 GC 含量上有差异。通过使用线性模型小波分析来研究在多个空间尺度上重组与基因组特征之间的关系，我们发现与着丝粒的距离在 512kb 尺度上存在显著的负相关，而基因密度和 GC 含量仅在 64kb 尺度上分别存在显著的正相关和负相关。重组与基因组特征之间的相关性，特别是与基因密度和多态性之间的相关性，表明它们是尺度相关的，需要在与这些特征的进化相关的尺度上进行评估。
