转录组测序揭示翼盖蕨(Didymochlaena trancatula)的全基因组复制历史

De novo transcriptome assembly reveals the whole genome duplication events of Didymochlaena trancatula

全基因组复制在动植物中普遍存在,被认为是促进物种进化的重要动力之一。作为蕨类植物的单种科物种,翼盖蕨(Didymochlaena trancatula)是真水龙骨类I的基部类群,在蕨类中具有独特的演化地位。本研究基于高通量测序,通过同义替换率(Ks)分析、相对定年分析揭示翼盖蕨的全基因组复制发生情况。Ks分析表明,翼盖蕨至少经历了两次全基因组复制事件,其中一次发生于59–62 million years ago (Mya),另一次发生于90–94 Mya,这两次全基因组复制事件分别和白垩纪第三纪的Cretaceous-Tertiary(C-T)大灭绝事件以及翼盖蕨的物种分化时间相吻合。进一步对两次全基因组复制保留的基因进行功能注释和富集分析,结果显示与转录及代谢调控相关的基因优势被保留。翼盖蕨的全基因组复制事件可能促进了该物种的分化及其对极端环境的适应性。

Whole genome duplication is an important driving force to speciation and evolution. Moreover, most existing plants and animals have experienced whole genome duplication in their evolutionary history. As the basal group of the Eupolypods I, Didymochlaena trancatula is the single fern species of Didymochlaenaceae. We performed transcriptome sequencing to detect whole genome duplication(WGD) events by analyzing age distributions built from synonymous substitution rates(Ks). We found that D. trancatula has experienced at least two WGDs during its evolutionary history. We dated the two WGDs at 59–62 million years ago(Mya) and 90–94 Mya, corresponding to Cretaceous-Tertiary(C-T) extinction event and the divergence time of D. trancatula, respectively. Annotation and functional enrichment analysis showed most duplicated genes that were retained are related to environmental regulation, further emphasizing the role that WGDs may play in the adaptive evolution of D. trancatula.