Chloroplast Genome Comparison And Phylogeny Of Primulaceae S.l.

Primulaceae s.l.is a large family in the Ericales with approximately 2590 species of 58 genera;they have higher adaptability and diversity,where they are distributed widely throughout tropical and temperate areas.The family have richness species,with many ornamental and medicinal plants and rapidly differentiated groups,as well as a model group for heterostyly—Primula L.The problem of the definition about the family has almost be solved,but there have some questions about the definition of subfamily and the systematic positions of some genera.Chloroplast genome is characterized by stable structure,moderate size and appropriate molecular evolution rate,which has been widely used in phylogenetic studies.In order to understand the phylogenetic and evolutionary relationships within Primulaceae s.l.,we conduct a comparative chloroplast genome analysis and phylogenetic analysis of Primulaceae s.l.taxa and estimated the divergence time of the family.The study is to add the data of chloroplast genome of this family,which will provide references for future study in this field.Main findings of this study are as follows: 1.Comparative chloroplast genome analysis of Primulaceae s.l.A total of chloroplast genomes of 70 samples from 65 species were obtained,which include 60 were sequenced and assembled in this study and some published data from NCBI.The size of the chloroplast genomes of the 70 Primulaceae s.l.species ranged from 150528 bp to 157241 bp,which have four-part structure,including an LSC region and an SSC region and a pair of IR regions.The Primulaceae s.l.chloroplast genomes contained 112-114 genes,including 78-80 protein-coding genes,30 t RNA and 4 r RNA genes,respectively.They were similar in gene structure,gene content and order,and GC content.It was shown that IR regions have lower divergence than SC regions,and 9 regions were highly variable.A total of 4661 SSRs were identified in the SSR analysis of 70 Primulaceae s.l.,and the mononucleotide SSR is the most,the hexanucleotide SSR is the least.2.Phylogenetic analysis of Primulaceae s.l.This is the first phylogenetic analysis of primulaceae s.l.at the family and subfamily levels based on chloroplast genome data.The results showed that the Primulaceae s.l.is a monophyly group has a good support.And Mrysinoideae in APG is a paraphyletic group.In our study,the results of phylogenetic analysis based on different chloroplast genome data sets and the most of single gene trees from conflict analysis of phylogenetic signals,support that Stimpsonia belongs to Primuloideae,rathan than in Myrsinoideae in the APG.The system location of cyclamen is not clear in our phylogenetic tree based on chloroplast genome.At the same time,the assisnment of Samolus to Theophrastoideae obtained a high support.3.Divergence time of Primulaceae s.l.Based on the method of select clock-like genes,the genes rpo B,ycf1,rpo C2 were selected to estimated the divergence time of Primulaceae s.l.The results showed that,the family's stem age is 75.2 Ma in the late Cretaceous,and the crown age is 68.56 Ma in the late Cretaceous,and at this time,the Maesoideae separated from other three subfamilies.Then the Theophrastoideae separated from the two remaining subfamilies at 61.03 Ma in the early Paleocene,and the divergence between Primuloideae and Myrsinoideae occurred at early Eocene 51.41 Ma.The time of divergence in each subfamily was: Theophrastoideae at 56.85 Ma,Primuloideae at 47.84 Ma,Myrsinoideae at 31.88 Ma,and the divergence time of the four species of the Maesoideae contained in our study began around 4 Ma.