A Phylogenomic Study On Nolinoideae Of Asparagaceae

Nolinoideae is a subfamily in the Asparagaceae of Asparagales,including seven groups,i.e.,Polygonateae,Ophiopogoneae,Convalariceae,Ruscaceae s.s.,Dracaenaceae,Nolinaceae,Eriospermaceae.The subfamily is a group defined by molecular phylogenetic results,a lineage with taxa highly differentiated in morphology and habitats as well as widely distributed all over the world.At present,phylogenetic studies in Nolinoideae are mainly based on cp DNA fragments and most of the systematic relationships of the groups were topologically conflicting in multiple studies.The phylogenomic scheme was used in this study with transcriptome sequencing for 15 representative groups from seven tribes in the Nolinoideae.These transcriptome data were used to reconstruct the phylogenetic framework for the subfamily.The important morphological traits of each species were collected to reconstruct the ancestral state based on the new phylogenetic framework,and the significance of the evolution process of morphological features to the complex system relations in the Nolinoideae was explored.The main findings are as follows:1.Through the next generation sequencing,transcriptome data was collected on 15 representative samples from seven subclades of Nolinoideae based on Illumina Hiseq 2000 platform.Considering that several groups of Nolinoideae have important medicinal and ornamental value,a comprehensive and detailed annotation of transcriptome data is therefore performed.NR annotation quantified the exogenous contamination of the transcriptome data sets used in this study,in which all the data sets contained only a small amount of exogenous contamination,which could ensure the follow-up high-quality analysis results.In addition,this study also included GO annotation,KEGG annotation and other commonly used annotation information.Transcriptome data for species such as Theropogon pallidus,Aspidistra fenghuangensis and Eriospermum lanceifolium have been sequenced for the first time,in particular,Aspidistra fenghuangensi is endemic to Wuling mountain area.2.In this study,based on massive transcriptome data,a total of 2124 sets of amino acid ortholog groups and corresponding coding sequence gene sets were screened through accurate screening steps of ortholog group.Three reconstruction strategies of phylogenetic framework were adopted: Maximum likelihood method,Bayes method and Coalescent theory.By comparing the topological structure of the species tree and the supermatrix gene tree,it was found that there was a conflict in the systematic location of the Theropogon pallidu.The statistics of single gene tree(maximum likelihood method)topological confirmed that the species tree was seriously affected by the topological conflict of gene tree in the construction process,and further confirmed the complex origin and evolution mechanism in the Nolinoideae.Therefore,the topological of the species tree lacks confidence in the response of the real phylogenetic relations among the various groups in the Nolinoideae.The topological structure of the combined gene tree fully reflects the phylogenetic framework of the seven main groups of Nolinoideae:(1)Eriospermum,(2)Dracaenaceae,(3)Ruscaceae s.s.,(4)Nolinaceae,(5)Ophiopogoneae,(6)Convallarieae,(7)Polygonateae.The phylogenetic position of the Eriospermum as the first branch at the base of Nolinoideae has been well supported for a long time,so as an out-group,Dracaenaceae,Ruscaceae s.s.,and Nolinaceae were distributed at the base of the system successively,presenting a grade distribution,among them,the Dracaenaceae is the first group to differentiate in the woody group,and the Ruscaceae s.s.is embedded between the Dracaenaceae and the Nolinaceae;The three herbaceous groups of Ophiopogoneae,Convallarieae,and Polygonateae merged into a monophyletic branc in the phylogenetic topology.The Ophiopogoneae was the first lineage,and the Convallarieae subsequently differentiated into a sister group with the Polygonateae.In addition,the long-standing phylogenetic dispute has been settled and the Theropogon pallidu has been placed in the Ophiopogoneae.All phylogenetic reconstruction strategies support the convergence of the phylogenetic position of the Maianthemum japonicum into the Polygonateae.3.Through extensive collection in Nolinoideae important morphological characters(life-form,location of flower,types of inflorescence,the types of rhizomes,abnormal stem type),through a reliable super-matrix gene tree is used for reconstruction of the ancestor state of Nolinoideae,but the character mosaic distribution phenomenon is more,so failed to determine the ancestor state of subfamily important traits.