Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai 201602, China.
Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai 201602, China.
Int J Mol Sci. 2019 Apr 19;20(8):1926. doi: 10.3390/ijms20081926.
Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous-Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, , for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site () between paralogs; age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a peak value of approximately 1.2 was obtained for both samples; however, the frequency distributions varied significantly. Importantly, we dated the WGD event at 51-53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as , which exhibits higher temperature tolerance.
全基因组加倍（Whole-genome duplications，WGDs）在植物中广泛存在，并且经常与全球气候变化事件同时发生，例如大约 6500 万年前的白垩纪-第三纪（Cretaceous-Tertiary，KT）灭绝事件。蕨类植物的基因组比种子植物更大，染色体数目也更高，这可能是由于多轮多倍体化的结果。在这里，我们使用模型蕨类植物 的二倍体和三倍体材料来检测 WGD。使用高质量的 RNA-seq 数据来推断同源基因之间每个同义位点的同义替换数（）；年龄分布和绝对日期测定方法用于确定 WGD 事件的年龄。两个样本均获得了约 1.2 的古代 WGD 事件的峰值证据；然而，频率分布差异很大。重要的是，我们将 WGD 事件定年在 51-53 mya，与古新世-始新世极热事件（Paleocene-Eocene Thermal Maximum，PETM）相吻合，当时地球比新生代的任何其他时期都更温暖和湿润。具有特定功能的重复基因（如环境反应）被优先保留，这进一步支持了这些重复基因可能促进了对环境变化的快速适应，并可能导致进化成功，特别是对于像 这样的泛热带物种，它表现出更高的温度耐受性。
