Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
University of Chinese Academy of Sciences, Beijing, China.
Genome Biol Evol. 2021 Jan 7;13(1). doi: 10.1093/gbe/evaa232.
Polyploidy can provide adaptive advantages and drive evolution. Amitotic division of the polyploid macronucleus (MAC) in ciliates acts as a nonsexual genetic mechanism to enhance adaptation to stress conditions and thus provides a unique model to investigate the evolutionary role of polyploidy. Mutation is the primary source of the variation responsible for evolution and adaptation; however, to date, de novo mutations that occur in ciliate MAC genomes during these processes have not been characterized and their biological impacts are undefined. Here, we carried out long-term evolution experiments to directly explore de novo MAC mutations and their molecular features in the model ciliate, Tetrahymena thermophila. A simple but effective method was established to detect base-substitution mutations in evolving populations whereas filtering out most of the false positive base-substitutions caused by repetitive sequences and the programmed genome rearrangements. The detected mutations were rigorously validated using the MassARRAY system. Validated mutations showed a strong G/C→A/T bias, consistent with observations in other species. Moreover, a progressive increase in growth rate of the evolving populations suggested that some of these mutations might be responsible for cell fitness. The established mutation identification and validation methods will be an invaluable resource to make ciliates an important model system to study the role of polyploidy in evolution.
多倍体可以提供适应优势并推动进化。纤毛虫中的多倍体大核（MAC）的无丝分裂作为一种非性遗传机制，增强了对胁迫条件的适应能力，因此为研究多倍体的进化作用提供了独特的模型。突变是导致进化和适应的变异的主要来源；然而，迄今为止，纤毛虫 MAC 基因组在这些过程中发生的新突变尚未得到表征，其生物学影响也尚未确定。在这里，我们进行了长期的进化实验，以直接探索模型纤毛虫嗜热四膜虫中 MAC 的新突变及其分子特征。建立了一种简单但有效的方法来检测进化群体中的碱基替换突变，同时过滤掉由重复序列和程序性基因组重排引起的大多数假阳性碱基替换。使用 MassARRAY 系统对检测到的突变进行了严格验证。验证后的突变显示出强烈的 G/C→A/T 偏向性，与其他物种的观察结果一致。此外，进化群体的生长速率逐渐增加表明，其中一些突变可能与细胞适应性有关。建立的突变识别和验证方法将成为一个宝贵的资源，使纤毛虫成为研究多倍体在进化中的作用的重要模型系统。
