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

Abstract

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.