Phylogenetic Study Of Rhodiola (Sedumaceae) Based On Plastid Genome

With the development of sequencing technology,a large number of plant plastid genomes have been sequenced,and widely used in the study of systematics,but the nature of plastome evolution during rapid radiations was largely unknown.In addition,it is not clear whether plastomes have undergone adaptive evolution to extreme habitats,and few studies have systematically studied the role of plastomes in adapting to high-altitude environments.The genus Rhodiola L.belongs to the family Crassulaceae,including about 70 species of perennial herbs(55 species in China).With the uplift of the Qinghai-Tibet Plateau,Rhodiola underwent rapid radiation and adapted to high-altitude habitats,making it a good system for studying the role of plastomes in rapid radiation and adaptation to high-altitude environments.Although the phylogenetic position of Rhodiola in the family Crassulaceae has been identified,the relationship within the genus has not been fully resolved.Therefore,this study selected Rhodiola as the study system to explore plastome evolution of the genus during the process of rapid radiative and adaptation to high-altitude environment.Based on the plastomes,the phylogeny and the spatiotemporal evolution pattern of Rhodiola was also reconstructed.1.Plastome evolution of RhodiolaIn this study,we sequenced,assembled,annotated and analyzed plastomes of 12 representative species of Rhodiola and 7 species from Crassulaceae.The main results and conclusions are as follows:(1)Structural variationBy comparing the plastomes of 19 newly obtained species with those of two published species(Sedum sarmentosum,Phedimus kamtschaticus),it was found that:1)plastomes of all species varied in a relatively small range:from 150,126 bp(S.sarmentosum)to 151,924 bp(R.fastigiata);2)all plastomes were highly conserved in terms of type and order of gene content,each encodes 134 genes,including 85 protein-coding genes,37 tRNAs,8 rRNAs and 4 potential pseudogenes;3)four repeats were detected in 12 Rhodiola species:microsatellite repeats(624 in total),tandem repeats,discrete repeats,and palindromic repeats.Most of them were distributed in the large single-copy region and the intergenic regions;4)there is slight contraction and expansion of the inverted repeats region,which occurred at the boundary between the inverted repeats region and the small single-copy region;5)genome-wide comparison and sequence polymorphism analysis showed that inverted repeats region and coding region were more conservative than single copy regions and non-coding region.(2)Adaptive evolutionBased on the maximum likelihood tree,when the genus Rhodiola was used as the foreground branch,three genes containing positive selection sites(rpl16,ndhA and ndhH)and a gene with a faster evolution rate(psaA)were identified by selection analysis.However,when the dioecy clade within Rhodiola was taken as the foreground branch,neither positive selection gene nor fast evolution rate gene was detected;2)In order to link habitat to the genes with positive selection and faster evolution rate,habitat and elevation differences between Rhodiola and outgroups as well as between two clades of Rhodiola were compared.The results of principal component analysis based on 19 environmental factors showed that there were niche differences between R.rosea and R.integrifolia and other groups on PC1,while there were niche differences between other species of Rhodiola and outgroups on PC2.The results of altitude comparison showed that there were significant differences in elevation between Rhodiola and outgroups,while the two clades within Rhodiola showed no differences of habitat and altitude.Thus,we propose that the products of these genes were probably involved in the adaptation of Rhodiola to high altitude environments such as high light and low CO2 concentration.2.Phylogeny of Rhodiola based on plastomesIn this part,the plastomes of 23 representative plants of Rhodiola and Phedimus aizoon as the outgroup were obtained.The main results and conclusions are as follows:(1)Phylogenetic relationship within RhodiolaPhylogenetic trees were constructed from 24 samples using maximum parsimony,maximum likelihood and the Bayesian inference,the results showed that except for the position of R.humilis in the maximum likelihood method and the other two methods,the other groups are consistent.Rhodiola can be divided into two clades,one comprised dioecious species,the other hermaphrodite species expect R.stapfii.Among the dioecious clade,all species were from sect.Rhodiola and sect.Chamaerhodiola.(2)Evolution of several key traits within RhodiolaCombined with the phylogenetic results,this study traced the evolutionary history of five key traits of Rhodiola.The results showed that elongated rhizome,old flower stems persist and dioecism were derived traits,and all had two independent origins.The dichasial cyme was the ancestral state,and the panicle,corymbiform and helicoid cymes evolved once,respectively.Leafy cauline leaves was the ancestor state,scaly cauline leaves had multiple origin.In addition,the four traits have no correlation except inflorescence.(3)Origin and distribution of RhodiolaBased on the molecular data,this study estimated that Rhodiola and its sister group Phedimus diverged at 20.91 million years ago(Mya),and differentiated into two cladesat 6.34 million Mya.Through the reconstruction of the ancestral distribution range of Rhodiola,it was found that Rhodiola originated in The Qinghai-Tibetan Plateau and the Hengduan Mountains region,and then spread to other regions.In this study,the structural variation and adaptive evolution of species were studied based on whole plastomic data of Rhodiola and outgroups.The results provide evidence for the non-neutral evolution of plastomes and increases our understanding of the mechanism of plant adaptation to high altitudes.Meanwhile,the results of this study are of great significance for understanding the phylogenetic relationships within Rhodiola,the origin of Rhodiola and the evolution of several important morphological characters.