Whole Genome Duplication Events In Ferns Based On Transcriptome Data

Ferns are the second largest group of vascular plants,which originated about 400 million years ago.Before angiosperms,they dominated the land plants of ancient earth and are still very important in today's ecosystem.The chromosome number of most ferns is very high,which may be the result of whole genome duplication.Based on the methods of phylogeny and synonymous substitution rate(KS),the whole genome duplication events of 69 species of Ferns belonging to 64 genera and 38 families were detected,and the possible relationship between the whole genome duplication events and species diversity of Ferns was studied.The results show that:(1)By phylogeny,we found 16 whole genome duplication events: three ancient events,which are common to the existing Ferns,3 orders and 7 families,at the level of fern order,the ancestors of the Ophioglossales ? Gleicheniales and Salviniales,experienced at least one whole genome duplication event,while the ancestors of Polypodiales experienced at least four whole genome duplication events,which provide strong evidence for many whole genome duplication events in the evolution of ferns.(2)By using the method of synonymous substitution rate KS,transcriptome data of 69 species of ferns were calculated one by one.It was found that there were traces of whole genome duplication in 45 species,including 8 orders and 25 families.The whole genome duplication events were found in Equisetaceae?Ophioglossaceae?Marattiaceae?Lygodiaceae?Salviniaceae?Cibotiaceae and Lindsaeaceae.A large number of whole genome duplication were found in Pteridaceae?Dennstaedtiaceae and eupolypods.The phylogenetic results verified each other and further verified that ferns experienced many whole genome duplication events in the evolutionary process.(3)Functional enrichment of the remaining genes showed that a large number of genes were related to regulation.duplication genes are preferentially reserved for specific functions,such as environmental response.Further support for repetitive genes may promote rapid adaptation to environmental changes,and may lead to successful evolution,especially for pantropic species,such as Acrostichum aureum.(4)Based on the in-depth analysis of KS value of Didymochlaena trancatula andAcrostichum aureum,it was found that Acrostichum aureum experienced at least two whole genome duplication events in the evolutionary process,with the occurrence time of 54 Mya and 99 Mya respectively;Didymochlaena trancatula has experienced at least two whole genome duplication events in the evolutionary process,with the time of 62 Mya and 90 mya.The whole genome duplication events of Didymochlaena trancatula and Acrostichum aureum are closely related to the species differentiation history and global environmental changes of these two species.Studies suggest that ferns have larger genomes and higher chromosome numbers than seed plants,which may be due to multiple polyploidization.This study provides molecular evidence for the occurrence of WGD in ferns and important clues for the evolutionary history of ferns.