Variation And Evolution Of Chloroplast Genome Of Representative Taxa In Dipsacales

As an important branch of angiosperms,Dipsacales contains many woody plants,mainly consisting of two families,49 genera and about 1,090 species,mainly distributed in the northern hemisphere and parts of the southern hemisphere.Lonicera is a major component of the Caprifoliaceae family.It has about 200 species and contains a large number of horticultural ornamental plants and medicinal plants.At present,the research about the species of Dipsacales and Lonicera is mainly concentrated in the field of ecology and Chinese medicine.At the same time,the research on the phylogeny of its species mainly uses some molecular marker sequences and morphological evidence,and does not explain the evolutionary relationship of Dipsacales and Lonicera within genomic level.The chloroplast genome is an important molecular tool for studying the evolution relationship because of its characteristics of small length,single parental inheritance,low nucleotide substitution rate,simple and conserved gene content and genomic structure.In this study,we sequenced and assembled the chloroplast genomes of ten species,and downloaded seven chloroplast genome sequences from Genbank,using bioinformatics methods for comparative genomics analysis,using different data sets and different softwares have constructed the evolutionary relationship of the order.Our research further enriches the chloroplast genome database of the Dipsacales species,and provides more molecular evidence for the evolution relationship of the Dipsacales.The main contents and results of this study are as follows: 1.The chloroplast genome structure variation and phylogenetic evolution of 14 Dipsaceae speciesThe results of assembling and annotating chloroplast genome sequences showed that: The chloroplast genome of Dipsacale is quadripartite circular DNA molecule;the total length of the chloroplast genome of the six Adoxaceae species is 157,074 bp-158,305 bp,encoding 129 functional genes,including 84 protein-coding genes,37 tRNA genes and 8 rRNA genes;the total length of the chloroplast genome of eight Caprifoliaceae species is 154,732 bp-156,874 bp,encoding 128 functional genes,including 82 protein-coding genes,accD pseudogene,the number of tRNA gene and rRNA gene are the same as Adoxaceae.The rpl2 and rpl23 genes was lost a pair of copies in the chloroplast genome of Caprifoliaceae,while the ndhF gene was lost in the chloroplast genome of Adoxaceae.Meanwhile,these genes are located at the IR/SC boundary,and there were significant differences between the two families at the boundary of IR/SC.The difference of chloroplast genome content among families is due to the expansion and contraction of IR region.In the repeated sequence analysis,we found that the number of dispersed repeats(Adoxaceae =37;Caprifoliaceae =384)was higher than tandem(Adoxaceae =34;Caprifoliaceae =291)in the cp genome of 14 Dipsacales species.In the selection stress analysis,19 genes with selected sites were detected,including atpA,atpB,atpI,rps3,rps7,rps14,rps15,rpl22,rpl32,psaA,psaJ,psbC,pabK,clpP,infA,matK,rbcL,ycf1 and ycf2 genes.We have constructed a phylogenetic tree of the order Dipsacales using a variety of methods and different datasets.The study proves that the Dipsacales contain two major branches(Adoxaceae and Caprifoliaceae)fromed the late Cretaceous to the early Tertiary,about 81.14 Myr.At the same time,the Viburnum and Sambucus of traditional Caprifoliaceae formed a single clade with other genus of Adoxaceae,and the differentiation of the genus occurred in the Eocene,about 47.16-34.02 Myr.The genus Adoxa,Tetradoxa and Sinadoxa have a relatively close evolutionary relationship,and the differentiation time is 15-16 Myr of the Miocene.Among the 11 species of Caprifoliaceae,the genus Weigela was the earliest differentiation,and the differentiation time was 61.71 Myr in the Paleocene.The differentiation of the Linnaeeae composed of Kolkwitzia amabilis and Dipelta floribunda occurred at about 39.79 Myr;Lonicera was finally differentiated,and its diversification mainly occurred after 19.05 Myr.2.The chloroplast genome phylogenetic evolution of seven Lonicera speciesThe results of assembling and annotating chloroplast genome sequences showed that: The chloroplast genome structure of Lonicera is similar to that of Caprifoliaceae.The total length of the chloroplast genome of seven Lonicera species was 154,513 bp to 155,545 bp.In its simple repeat sequence(SSR)analysis,the number of mono-nucleotide repeat types is the highest,followed by the tetra-nucleotide repeat type,di-nucleotide,tri-nucleotide,hexa-nucleotide and penta-nucleoside repeat type.At the same time,we identified 18 variant hotspots(rps15,rps16,rps18,rpl23,psaJ,infA,ycf1,trnN-GUU-ndhF,rpoC2-rpoC1,rbcL-psaI,trnI-CAU-ycf2,psbZ-trnG-UCC,trnK-UUU-rps16,infA-rps8,rpl14-rpl16,trnV-GAC-rrn16,trnL-UAA intron and rps12-clpP),we used paml software to detect the selected sites of genes in the chloroplast genome of seven species,fourteen genes were detected,including two genes of ribosomal protein subunits(rps7 and rpl22),three genes of photosystem protein subunits(psaJ,psbC and ycf4),three NADH oxidoreductases Genes(ndhB,ndhH and ndhK),two subunits of the ATP gene(atpA and atpB),and four other genes(infA,rbcL,ycf1 and ycf2).For phylogenetic analysis of Lonicera,L.tragophylla,as a component of the Lonicera subgen.Lonicera,forms a sister branch with six other species of Lonicera.L.nervosa,L.ferdinandii,L.japonica and L.fragrantissima var.lancifolia belong to different subsect of Lonicera subgen.Chamaecerasus,respectively forming a single branch,while L.stephanocapoa and L.hispida belong to the Lonicera subsect.Bracteatae.