Plastid Phylogenomics And Biogeography Of Paris

Paris L.(Melanthiaceae)is a plant genus with significant economic importance.However,the phylogeny and biogeographic history have been questionable and contrioversial for a long time.In the present study,38 complete plastomes and nuclear ribosomal sequences(rDNA)of Melanthiaceae(33 species of Paris)were sequenced.The characteristics of the whole plastomes were revealed by comparing the structure.Phylogenetic analyses were preformed based on the plastome(including 9 published sequences of Melanthiaceae)and rDNA DNA sequences to elucidate the phylogenetic relationship of the family Melanthiaceae and Paris.The origins and biogeographic patterns of Paris were futher illustrated by molecular dating and biogeographic reconstruction of the genus Paris.The evolutionary history of genomic gigantism in Paris was investigated.In addition,the nucleotide substitution rate was analyzed based on the phylogenetic relationship.1.Comparative genomicsThe plastome of Paris,highly conserved,was a circular DNA molecule consisting of a large single copy region(LSC).a small single copy region(SSC)and two inverted repeat regions(IRs).The toal length and GC contens of all plastomes were 155,957-158,643 bp and 37.20%-37.70%,respectively.The plastome of Paris possessed 114 unique genes(80 protein-coding genes,30 tRNAs and 4 rDNAs)without obvious gene deletion and sntructural rearrangement.Among these unique genes,cemA and ycf15 were identified as a pseudogene in all Paris plastomes.It is noteworthy that the pseudogenization of the cemA gene also occurred in Trillium plastomes.which might be a molecular synapomorphy of Parideae.Comparatively,characterized by the IRA/LSC boundary falling into rps3.the significant IR expansion has only been found in Melanthiaceae to date.The expansion of IRA into the pseudogene of ycfl,but the overlap between the ycfl pseudogene and ndhF was only occurred in Sect.Kinugasa.The IRB region gradually expanded into the ycfl gene with the evolution of Paris.In addition,five plastome markers with relatively high levels of variation were identified from the plastomes:ndhF,ycfl,rpl23-ycf2,ycf15-trnL_CAA and trnN GUU-ycfl.2.Phylogenetic analysisThe conflict between rDNA and plastome topologies can be attributed to ancient intergeneric hybridization(Paris and Trullium),ancient and recent intersectional hybridization(Sect.Euthyra and Sect.A.xiparis)and incomplete lineage sorting or interspecific hybridization(Sect.Euthyra)by analyzing the species history and morphological characteristics.The phylogenetic analyses based on the whole plastomes recovered five well-supported lineages(Melanthieae,Chionographideae.Heloniadeae,Xerophylleae and Parideae)within Melanthiaceae.Pairis was resolved as strongly supported monophyly,.which is sister to Trillium.Therefore,it should be treated as a sinsle genus in taxonomy.Subgen.Daisya and Subgen.Paris in the classification system of Li(1984.1998)were not supported,and we suggested to cancel the classification level of subgenus.Sect.Euthyra,Sect.Dummianae,Sect.Fargesianae and Sect.Marmoata not were monophyletic,respectively.Therefore,warrant the four sections into the Sect.Euthyra.The results suggested that Paris should be divided into five sections:Sect.Euthyra,Sect.Axiparis,Sect.Thibeticae,Sect.Kinugasa and Sect.Paris.In addition,phylogenetic analysis showed that P.polyphylla and its varieties were not monophyletic.Therefore.we recommend that P.polyphylla var.chinensis,P.polyphylla var.yunnanensis,and P.polyphylla var.stenophylla were regarded as four distinct species instead of varieties.3.Distribution and divergence timesBased on the phylogenetic relationship,the divergence times of Melanthiaceae was estimated and the ancestral distribution area of Paris was reconstructed.The results showed that the most recent common ancestor(MRCA)of Paris might originated in northeastern Asia and northern China.Divergence of slender and thick rhizome clades was dated at 37.9 Mya,near the Eocene/Oligocene boundary,and subsequently migrated into Europe and subtropical East Asia.Under the climate and geological events of orogeny of Circum-Pacific around the Oligocene/Miocene boundary.the enhancement of Asian summer monsoon since the middle Miocene.Qinghai-Tibet Plateau(QTP)rose from the Late Miocene to the early Pliocene and glacial/interglacial cycles during the Pleistocene,a significant isolation and diverse habitats were formed,which is expected to have driven the diversification of a wide spectrum of pairis lineages.4.The evolution of the genomic gigantism in Paris japonicaAt present,we have found only three species(T.×hagae,T.rhombilolium and P.japonica)with genome sizes 1C>100 pg which have been found in the Melanthiaceae.Phylogenomic analysis and divergence estimation indicated their giant genomes may have originated from a common ancestor of Paris and Trillium and the genome size expansion in the MRCA was most possibly a gradual process that lasted for approximately 10 million years.In addition,the maritime climate of the Japan Islands would create relatively more humid habitats in which P.japonica can maintain the genomic gigantism after the opening of the Japan Sea separated the Japan Islands from the continent of Asia around the transition of the Oligocene/Miocene boundary(27.63 Mya).5.The divergences of plastome protein-coding genesThe analysis of nucleotide substitution rate(?)revealed accD,ccsA,clpP,ndhD,nclhF,ndhG.pet A.petB.rbcL,rpl2.rpl20,rpoA,rpoB,rpoC1.rps2.ycf1.ycf2,atpF,ndhA,ndhB,ndhC,ndh1,petD,p.shC?psbD.psbE.psbN.rpl16.rpl32,rpoC2,rps3,rps7,rps8,rps12 and rps14 genes of five sections of Paris(dN/dS>1)may have undergone positive selection during the evolutionary process of Paris.