| The plant genus Paris L.belongs to the family Melanthiaceae,whichcontains over 40 species,widely distributed in regions of the Eurasian continent from the temperate zone to the tropics.Moreover,it is an endangered medicinal plant in China.Since the establishment of the genus Paris,there have been differences in the classification of this genus.Many scholars also have different views on the genetic relationship between Paris.In addition,several rare new species have been found in recent years.The taxonomic status of these species is not clear,and the chloroplast genomes are lacking.The confusion of classification and the lack of biological information make the work of resource protection,development,and utilization impossible,whichseriously restricts the sustainable development of the related pharmaceutical industry.Therefore,we sequenced and assembled the chloroplast genomes of Paris species and Trillium tschonoskii.Comparative genomics was used to explore the evolutionary characteristics of chloroplast genomes of different species.Based on the sequence of protein-coding genes,complete chloroplast genome,and intergenic region,we constructed the phylogenetic trees of the genus Paris.It provides insights into the taxonomy of the genus from different perspectives and provides valuable data for exploring the evolutionary direction among species.The main results are as follows:1)The complete chloroplast genomes of 21 Paris species were obtained.P.lihengiana,P.caojianensis,P.polyphylla var.alba,P.polyphylla var.stenophylla,P.fargesii var.brevipetalata,P.polyphylla var.nana,and P.nitida were sequenced for the first time.It greatly enriched the genetic resources of the genus.At the same time,the phylogenetic location of these species is determined,whichprovides a theoretical basis for their resource protection and sustainable utilization.2)In this study,we analyzed the causes of higher AT content than GC content in the chloroplast genomes of Paris and T.tschonoskii.i.The most simple repeat sequence（SSR）is mononucleotide repeat,and most are A/T repeats.ii.The codon exhibited a strong bias toward an A or T at the third position.iii.The statistical results of RNA editing showed that all the predicted editing sites were C-T conversion.These phenomena greatly enrichthe content of bases A and T in the chloroplast genome.3)In this study,the coding genes of the chloroplast genomes of Paris and T.tschonoskii are counted.The results showed that the type,number,and order of genes in the chloroplast genome of the genus Paris were utterly consistent.The chloroplast genomes of 21 Paris species encode 135 genes,including 89 protein-coding genes,eight rRNA genes,and 38 tRNA genes.T.tschonoskii chloroplast genomes encode 130 genes,including 87 proteincoding genes,37 tRNA genes,and six rRNA genes.We found that chIB,chIL,ycf68,trnSUGA,and trnT-UGU genes were lost in Paris.4)The RNA editing of Paris and T.tschonoskii was studied for the first time.We found the second base C of ndhD gene in P.mairei,P.polyphylla var.alba,P.polyphylla var.nana,and P.nitida must transform into T to form the initiation codon ATG（M）and complete transcription and translation.5)The chloroplast genomes of 21 Paris species are highly conservative,and there is no rearrangement and recombination.The comparison showed that the variation of the noncoding region was higher than the protein-coding region,LSC region,and IR region was higher than that of SSC region.The boundary analysis showed that P.polyphylla var.polyphylla had the most significant variation.Compared with other species,the IRs area of P.fargesii var.petiolata,P.polyphylla var.alba,P.lihengiana,and P.dulongensis have apparent contractions.6)Ka/Ks analysis showed that clpP,ndhA,ndhF,rpl20,rpl32,rpoC1,and ycf2 have diverged in Paris.Among them,ndhF evolved in P.dulongensis,P.verticillata,P.quadrifolia,and P.japonica.The cold climate may cause this phenomenon at high latitudes and altitudes.These species can adapt to changing habitats through the adaptive evolution of ndhF.7)All phylogenetic trees showed that Paris was closely related to Veratrum,so it should be classified into the Melanthiaceae family.The protein-coding genes tree and chloroplast genomes tree supported the Paris should divide into three subgenera with five sections（Subgen.Euthyra: Sect.Euthyra,Sect.Axiparis,Sect.Thibeticae,and Sect.Kinugasa,Subgen.Trillium,and Subgen.Paris s.s.: Sect.Paris）.IGS tree shows that Paris was a nonmonophyletic genus composed of two independent genera,Daiswa and Paris s.s..Therefore,Paris should be divided into two separate genera.Moreover,both classification systems indicated that the seven species sequenced for the first time belonged to Sect.Euthyra and both predicted that the species in Sect.Axiparis might be the alternative resource for Paridis Rhizoma. |
