Molecular Phylogeny And Classification Revision Of Stachyuraceae

The species concept plays an important role in the study of taxonomy,biological evolution,and biodiversity.And it will have affection on species definition as well as biodiversity protection to correctly understand species concept.In the molecular systematical studies of some difficult groups,limited sampling and insufficient information sites often lead to the difficulty of species definition.With the decrease of sequencing cost,chloroplast genome has been widely used in phylogenetic research,which provides sufficient information sites for solving the phylogenetic relationships among difficult groups.However,the materials of genome sequencing are often collected from fresh or silica gel dried leaf,and the high cost of sampling limits the number of samples.In order to clarify species definition of difficult groups at a lower cost,this study explores a systematic genomics method based on specimen materials,which overcomes the shortcomings of sampling difficulties and insufficient information loci.In this study,Stachyuraceae,which has been controversial in the definition of species,was selected as the research taxa.Specimen materials sampled at the population level were obtained from the herbarium of the institute of botany,Chinese academy of sciences(PE).To obtain high-quality DNA template,the DNA reconstruction technology was used to repair the short DNA fragments in the specimen material.Then,based on the complete chloroplast genome sequence,we found the high-variation regions of Stachyurus,and amplified these regions for phylogenetic analysis.Stachyuraceae,endemic to east Asia,contains only one genus,Stachyurus.On account of the large variation in the morphological characters,the classification of Stachyurus has been controversial in previous taxonomic studies.In this study,we collected 69 individuals of Stachyurus from PE,representing the species,geographical and morphological diversity of the genus.Firstly,using four chloroplast DNA markers and one ITS fragment,we conducted the phylogenetic analysis of Stachyurus.Then,based on the phylogenetic tree,we selected four representative individuals for whole chloroplast genome sequencing.By comparing the chloroplast genome sequence,we found 44 high variation area.Finally,we obtained a combined data sets including 44 chloroplast DNA and one nuclear DNA(ITS)of 69 individuals.Boswellia sacra and Leitneria floridana were selected as outgroup.Using the Maximum Likelihood method and Bayesian method,we reconstructed the phylogenetic relationships of Stachyurus.The results showed that Stachyurus was divided into five highly supported clades,each clade corresponding to a specific distribution.The relationships within Stachyurus are also well resolved.Combining the molecular,geographic and morphological data,we revised the classification of Stachyuraceae.Finally,we identified seven species and one doubtful species for this family.To sum up,the systematic genomics method based on specimen materials is valid to validvalidvalid resolve the phylogenetic relationships of Stachyuraceae,as well as define the species boundries of this family.This study provides an economic and effective method and research paradigm for solving the phylogeny and species definition of difficult taxa.