A Study On Phylogenomics Of Gleicheniaceae And Its Related Taxa

Lycopods and ferns are the first land vascular plants with spore propagation,dating back more than 400 million years of evolutionary history.Its special evolutionary position is of great significance to study phylogeny and ecological change of the plant kingdom.Over the past 20 years,the use of molecular systematics has led to a deeper understanding for the evolution of Pteridophyta.However,the phylogenetic relationship still exists a lot of controversy in a few key nodes.In the basal leptosporangiate,for example,the evolutionary relationship of the Gleicheniaceae and its related taxa is still up in the air.In this study,we firstly used five chloroplasts loci to analysis the molecular phylogeny for 128 samples of Gleicheniaceae and reconstructed their evolutionary relationship.And then we used phylogenomic method to reconstruct the evolutionary history of Gleicheniaceae and its related taxa by using maximum likelihood with multiple representative taxa.The main results of this study are as follows:1.Diplopterygium simulans and Dicranopteris linearis are independent species.We reconstructed the phylogenetic relationship of Gleicheniceae with Neighbor-Joining(NJ)and Maximum Likelihood(ML)methods based on five chloroplasts loci(rbcL,atpB,rps4,matK and trnL-F),using Dipteridaceae and Matoniaceae as outgroups.The results showed that six genus of Gleicheniaceae were divided into two groups,Diplopterygium,Dicranopteris and Gleichenella were grouped into an independent monophyly,Sticherus,Gleichenia and the monotypic genus Stromatopteris,which only distributed in New Caledonia,were another group.Further analysis of Diplopterygium,the results show that Diplopterygium laverissimum and Diplopterygium bancroftii in Central America were the basal group of the genus.D.simulans,as an independent species,was the sisterhood with Diplopterygium cantonense and should not be incorporated into Diplopterygiumgiganteum,it also implied that there were still a large number of species waiting to be“re-discovered” in the synonyms.Further analysis of Dicranopteris,we found that D.linearis and Dicranopteris pedata were independently grouped into a monophyly,therefore they should be two independent species and D.linearis should not be incorporated into D.pedata.The results of DNA barcode showed that rbcL,matK and trnL-F are the ideal DNA barcodes for distinguishing the plants of Gleicheniaceae,and the combined analysis is more effective for species identification.2.Gleicheniaceae and Hymenophyllaceae are sisterhood.In this study,we selected 25 samples include six species of three genus of Gleicheniaceae,11 species of six genus of Hymenophyllaceae,two species of two genus of Dipteridaceae and six outgroups.After the analysis of RNA sequencing,assembling and de-redundancy,we screened 2,398 "one-to-one" orthologous genes,trimmed to obtain the conserved regions of the sequences,combined conserved sequences in series to obtain a supermatrix,including 260,710 amino acid sites.And then we re-infer the evolutionary relationship of the Gleicheniaceae and its related taxa based on the maximum likelihood method with the optimal model(JTT + F).The results showed that Gleicheniaceae and Hymenophyllaceae were sister groups,and then the two species were grouped into a monophyly with Dipteridaceae(BPML =100).The rhizome of these three family plants is long-repent,and the plants have the ability of clone reproduction and usually formatted a large populations;the flora of Dipteridaceae are terrestrial,single leaves,some existing plants of Gleicheniaceae are climbing or semi-epiphytic,and the vast majority of Hymenophyllaceae are epiphytic,it presumed that Gleicheniaceae and its close groups were divided in the early period,one adapted in the dry and sunny environment,another one adapted in the dark and damp environment,this may be related to the emergence of a large area of hot and humid forest in the Carboniferous.3.Meringium should not be incorporated to Hymenophyllum,and Selenodesmium is not a monophyly.The family Hymenophyllaceae was divided into two groups,Hymenophylloids and Trichomanoids.Hymenophyllum barbatum,Mecodium badium,Mecodium osmundoides and Microtrichomanes digitatum were grouped into a monophyly,which support that Mecodium and Microtrichomanes were belong to the genus Hymenophyllum in Flora of China(English edition,2013).Meringium denticulatum was sister to Gonocormus minutus and was not group into the Hymenophylloids,soMeringium should not belong to the genus Hymenophyllum.Selenodesmium obscurum was sister to Cephalomanes sumatranum and was paraphyly with Selenodesmium siamense.Based on this result,Selenodesmium is not a monophyletic group and maybe only a part of Selenodesmium belong to Abrodictyum.In this study,however,the taxa of these group is not enough,and these problem should be solved by increasing the number of taxa in further study.This study reconstructed the phylogenetic relationship of Gleicheniaceae and its related taxa using chloroplast and transcriptome data,clarified the internal evolutionary relationship of Gleicheniaceae,resolved the controversy of the basal leptosporangiate,and provided evidence for further understanding the classification and evolution of lycopods and ferns.