Development Of Single-copy Nuclear Gene Makers And Phylogenetic Study Of Sparganium (Typhaceae)

Sparganium(Typhaceae)is an important genus of aquatic plants,which is widely distributed in temperate and cold regions of the Northern Hemisphere.Clarifying the phylogenetic relationship of Sparganium is helpful to infer the evolutionary history of Sparganium,and thus to deeply understand the origin and evolution of aquatic plants in the north temperate zone.In this study,the transcriptome of S.fallax was sequenced and single-copy nuclear genes suitable for Sparganium were developed based on transcriptome data.On the basis of extensive sampling,the phylogenetic reconstruction of Sparganium was carried out by using both single-copy nuclear genes and chloroplast DNA fragments.Furthermore,the phylogenetic relationship between species and the taxonomic status of some species or subspecies were discussed.The results are as follows:1.A total of 646.66 M high quality data were obtained from transcriptome sequencing of S.fallax.After de novo assembly,152111 credible transcripts were acquired.Compared with some major databases including Swiss-Prot,52.18%(79,376)of transcripts were annotated.2.Three single-copy nuclear loci with good amplification effect and suitable polymorphism were successfully developed using the transcriptome of S.fallax,which have more information loci and higher resolution than chloroplast genes,providing a powerful tool for the phylogenetic study of Sparganium.2.Three single-copy nuclear loci with easy amplification and suitable polymorphism were successfully developed based on the transcriptome of S.fallax,which have more informative sites and higher resolution than chloroplast DNA fragments,providing a powerful tool for the phylogenetic study of Sparganium.3.Phylogenetic reconstruction of 83 samples from 16 species of Sparganium showed that this genus was divided into 2 major clades.Clade ? included S.eurycarpum,S.erectum,and S.stoloniferum,and Clade ? included the remaining 13 species of Sparganium.Clade ? consisted of two branches.One branch included three species: S.natans,S.hyperboreum,and S.probatovae,and the other branch included 10 species,which could be further subdivided into four subbranches: S.americanum+S.androcladum,S.gramineum+S.fluctuans,S.fallax+S.subglobosum,and S.japonicum +S.glomeratum+S.emersum+S.angustifolium.However,the phylogenetic relationship of these four subbranches had the phenomenon of cytonuclear discordance.4.Further analysis of the phylogenetic relationship within each clade showed that both S.eurycarpum and S.emersum are not monophyletic group,indicating their taxonomic status needs to be further studied.Individuals from each subspecies S.erectum subsp.microcarpum,S.emersum subsp.acaule,and S.stoloniferum subsp.choui formed a clade,respectively,and were distinct from the original species.We thus suggested that their previous treatments as subspecies were inappropriate.They should be classified as species again with their names S.microcarpum,S.acaule,and S.choui,respectively.