INRA, UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, 63100 Clermont Ferrand, France.
Genome Res. 2010 Nov;20(11):1545-57. doi: 10.1101/gr.109744.110. Epub 2010 Sep 28.
The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5-12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.
比较当今物种的染色体数量与常见的重建古祖先，引发了人们对哺乳动物染色体随时间发生重排的强烈猜测。然而，由于缺乏与进化变焦相关的基因组序列的相关实例，类似的关于植物基因组进化以及导致镶嵌同线性块的分子机制的研究在植物中一直缺乏。此类研究需要属于同一科但分化为不同亚科的物种的基因组。我们最重要的作物属于禾本科，其中许多基因组现已测序。基于详细的古基因组学，使用 n = 5-12 个草类祖先染色体组（AGK）的基因内容和顺序推断，我们描绘了包含来自水稻、玉米、高粱和拟南芥基因组中同源区域完整一套连接断点的序列间隔，代表三个不同的亚科和不同的多倍化事件。通过关注这些序列间隔，我们可以表明，来自 n = 12 个共同古祖先的染色体数量减少是由非随机着丝粒双链断裂修复事件驱动的。似乎非同源染色体之间的着丝粒/端粒的非法重组导致了嵌套染色体融合（NCFs）和同线性断裂点（SBPs）。当比较包含 NCF 的间隔的结构时，我们得出结论，SBPs（1）是减数分裂重组热点，（2）对应于通过重复入侵的高序列转换位点，（3）可能被视为产生适应性表型的新的进化热点的热点。
