Chloroplast Genome Variation And Phylogeny Analysis Of Dipelta

Dipelta belongs to Caprifoliaceae and is endemic to China.It is one of the ancient and relic woody genera in North Temperate flora.The genus is distributed in the southwest of China,north to Shaanxi and Gansu,east to Hubei,western Hunan and Eastern Guangxi.There are only three species in the genus,namely D.floribunda,D yunnanensis and D.elegans.Among them,D.yunnanensis and D.elegans are vulnerable and endangered species.At present,most of the studies about the genus Dipelta are based on concatenated gene fragments,and there is no complete chloroplast genome data to support the evolution of species in the genus.D.elegans,as earliest differentiated species,has been reported.However,the study on the divergent time of D.floribunda and D.yunnanensis is lacking,which also need more data to explore.Due to the limited information obtained from chloroplast fragments,it is not conducive to the study of species variation and interspecific relationship.In this study,the complete chloroplast genome data of 14 individuals from 3 species of Dipelta were obtained by high-throughput sequencing technology for the analysis of DipeltaIn addition,we also annotated the internal transcribed spacer(ITS)sequence and some mitochondrial genes of all individuals for comparative analysis of phylogenetic relationships in the genus Dipelta.The divergent time of Dipelta species was estimated with two fossil sites based on chloroplast genome.The main results are as follows:(1)Fourteen chloroplast genomes of the Dipelta exhibited a typical quadripartite structure with a total length of 15514 bp-155948 bp,including a pair of inverted regions(IRs)(23201-23496 bp),a large single copy region(83733-89975 bp)and a small single copy region(18952-19117 bp).Each genome encodes 128 genes,including 82 protein-coding genes,37 transfer RNA genes(tRNA)and 8 ribosomal RNA genes(rRNA).Fifteen of these genes were duplicated in IRs.Amino acids and codon usage were coincident among the 14 chloroplast genomes of Dipelta,both prefer to use A and T bases.By making general comparisons on three data,we found that the plastomes were conserved in genomic structure,gene order and gene contents,but with highly variable repeat sequences.By using mVISTA analysis and mutation rate statistics of coding and non-coding regions in 14 individuals of the genus Dipelta,five genes and four intergenic spacers displayed the greatest variability.The comparison of the IR/SC boundaries showed that the differences were not significant The structural variation mainly occurred in the rpl23 gene located in the LSC/IRb region.In addition,the genes of rpl23,ycfl and ycf2 were identified under positive selection pressure by using site-specific model(2)The phylogenetic trees based on the whole chloroplast genome data and the combined data of 12 mitochondrial genes identified the status of three species of Dipelta,and the D.floribunda and D.yunnanensis were sister groups.Phylogenetic trees based on ITS sequences indicate that D.floribunda may hybridize with D yunnanensis.The molecular divergence dates based on chloroplast genomes indicated that Dipelta originated in the Eocene(about 38.69 Ma)and D.elegans was the basal taxon.Interspecific divergences were estimated at about 33-37 Ma in the Eocene/Oligocene boundary.Based on the above studies,we speculated that modern Dipelta may be a paleoendemic genus,and the species divergence was an ancient event.