Table_1_Angiosperm-Wide and Family-Level Analyses of AP2/ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication.XLSX

Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.

植物因其不动的特性而常常遭遇严苛的环境压力，这促使调控环境响应的基因发生进化。此类进化主要通过基因复制及其后续分化来实现。在调控植物环境响应与发育过程中，AP2/ERF基因家族扮演着至关重要的角色；然而，这些基因在被子植物以及适应不同生态位的主要被子植物科中的进化历史尚不明确。具体而言，关于在若干植物科起源时期发生的全基因组复制事件对基因拷贝数的影响尚属未知。在本研究中，我们首次对被子植物AP2/ERF基因进行了全被子植物范围的比较研究，识别出75个被子植物直系同源群（AOGs），每个同源群均源自一个原始被子植物基因拷贝。在这些同源群中，有21个在许多被子植物谱系中保留了拷贝数增加的副本，而其余的54个同源群则倾向于维持较低的拷贝数。对十字花科多个物种的进一步分析表明，该科特有的副本在编码区经历了差异性的选择压力，其中某些同源基因表现出正向选择的迹象。此外，在拟南芥中，顺式调控元件在副本之间也表现出广泛的分化。进一步的，表达水平的比较表明，经常保留副本的AP2/ERF基因具有广泛的表达模式，这为通过改变表达模式实现功能多样化提供了更多机会，并在某些AOGs中提供了一种重复保留副本的机制。我们的结果代表了AP2/ERF基因家族最全面的进化历史，并支持了以下假说：具有更广泛表达模式的AP2/ERF基因比具有较窄表达谱的基因更有可能作为副本被保留，这可能导致副本基因亚功能化的几率更高。某些AOGs倾向于保留副本，允许表达和功能的分化，这可能有助于适应新的环境条件，从而促进复杂信号网络的进化。