State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
J Mol Evol. 2010 Feb;70(2):137-48. doi: 10.1007/s00239-009-9316-4. Epub 2010 Jan 1.
Although plant resistance (R) genes are extremely diverse and evolve rapidly, little is known about the mechanisms that generate this sequence divergence. To investigate these forces, we compared all nucleotide binding sites and leucine-rich repeat R-genes between two closely related species, Arabidopsis thaliana and Arabidopsis lyrata. Our analyses revealed two distinct evolutionary patterns driven by either positive or stabilizing selection. Most R-genes (>50%) were evolving under strong positive selection characterized by high Ka/Ks ratios (>1), frequent recombination, copy number variation, and extremely high sequence divergence between the two species. The stably selected R-genes (<30%) have exactly the opposite four characters as the positively selected genes. The remaining R-genes (about 20%) are present in only one genome and absent from the other. A higher proportion of such genes were found to be part of TNL class (23.5%) compared to the non-TNL class (5.6%), suggesting different evolutionary patterns between these two groups. A significant correlation between Ka and divergence was revealed, indicating that the rapid evolution and diversification of R-genes were initiated by selectively generated, frequently shuffled and selectively maintained non-synonymous substitutions. Our genome-wide analyses confirmed an amazing mechanism by which plants to selectively accumulate and efficiently exploit these non-synonymous substitutions for their resistance to various pathogens.
尽管植物抗性 (R) 基因极其多样化且快速进化，但对于产生这种序列差异的机制知之甚少。为了研究这些力量，我们比较了两个密切相关的物种——拟南芥和拟南芥 lyrata 之间的所有核苷酸结合位点和富含亮氨酸重复的 R 基因。我们的分析揭示了两种由正选择或稳定选择驱动的截然不同的进化模式。大多数 R 基因（>50%）在强正选择下进化，其特征是 Ka/Ks 比值较高（>1）、频繁重组、拷贝数变异以及两个物种之间的序列高度分化。稳定选择的 R 基因（<30%）具有与正选择基因完全相反的四个特征。其余的 R 基因（约 20%）仅存在于一个基因组中，而在另一个基因组中不存在。与非 TNL 类（5.6%）相比，此类基因中有更高比例（23.5%）属于 TNL 类，表明这两组之间存在不同的进化模式。Ka 与分化之间存在显著相关性，表明 R 基因的快速进化和多样化是由选择性产生、频繁改组和选择性维持的非同义取代引发的。我们的全基因组分析证实了一种惊人的机制，即植物选择性地积累并有效地利用这些非同义取代来抵抗各种病原体。
