A Phylogenomic Approach To Resolve The Relationships Of Dennstaedtiaceae Based On Transcriptome Sequencing

Dennstaedtiaceae represents one of the basal groups in Polypodiales,with about 265 species in 10 genera,which are widely distributed in tropical and subtropical regions.This group is remarkable,due to the taxonomic category of this family is controversial among different classification systems,in which its comprising genera are from 10 to 16.Previous phylogenetic studies of Dennstaedtiaceae and its related taxa are mainly based on the chloroplast or nuclear genes,although some phylogenetic relationships have been resolved,some are still unclear,including the relationships among Dennstaedtiaceae,Pteridaceae and Eupolypods within the Polypodiales,as well as the intergeneric relationshipe within the Dennstaedtiaceae.In recent years,with the rapid development of high-throughput sequencing technology,phylogenomics has provided the most effective method for the non-modal plants phylogenetic analysis.In this study,based on a large-scale sampling was performed on Dennstaedtiaceae and its related taxa,20 samples were obtained,covering Dennstaedtiaceae,Pteridaceae,Eupolypods,Lindsaeaceae and Cyatheaceae.Through transcriptome sequencing,we obtained 92.3 Gb raw data.After filtering and de novo assembly,we obtained 1,514,657 unigene,and then predicted 951,017 open reading frames(ORFs).Gene family clusters across the 20 species were identified according to bidirectional blast of protein sequences,then a total of 664 one-to-one orthologous genes were selected by gene tree method,in which,66 genes are found single-copy.The phylogenetic analysis was performed with concatenated and coalescent methods respectively with two different supermatrixs,a consistent topology with higher bootstrap support were obtained.The results strongly support that Dennstaedtiaceae is sister to Eupolypods,and Dennstaedtiaceae can be divided three clades: Monachosorum forms an independent clade;Dennstaedtia and Microlepia form a clade;and the rest genera form another clade.At the same time,we rebuild the phylogenetic network of Dennstaedtiecaea and its related taxa.The results show that these groups exists complex reticulate evolution relationship,and Dennstaedtiaceae can be divided three clades which present the complex evolution relationship.By calculating synonymous substitution rates(Ks values)method to detect the whole genome duplication events of Dennstaedtiaceae and its related taxa,we inferred that the 3 representative of Dennstaedtiaceae maybe undergo a whole genome duplication event according to the Ks frequency distribution results.This study successfully resolved the evolutionary position of Dennstaedtiaceae in Polypodiales,and rebuilded their intergeneric phylogenetic relationships.The results provide a basis for further study the morphogenesis and evolution of both ferns and terrestrial plants.The whole genome duplication event study shows that the common ancestors of Dennstaedtiaceae may have undergone whole genome duplication.It can provide reference for the study of species differentiation and adaptive evolution of Dennstaedtiaceae.