Chloroplast Genome Sequences Of Vitis:Structural Organization And Phylogenetic Analyses

The economically important grape family(Vitaceae)are widely distributed and has numerous ornamental value.In recent years,this family has been subjected to different phylogenetic studies.At present,most of known chloroplast genome sequences grew rapidly in angiosperm families.Comparing the complete chloroplast genome sequence of different species and analyzing the difference of 4 border positions are helpful to find the difference of chloroplast genome sequence and understand the evolution process between species.Furthermore,the very conserved sequence and the slow rate of nucleotide substitution for the chloroplast DNA make it an ideal data for phylogenetic studies.In the present study,the chloroplast genome of 11 species of grape were sequenced by Illumina next-generation sequencing technique.In order to evaluate the chloroplast genome evolution,we compared 16 complete chloroplast genomes including Ampelopsis glandulosa var.Brevipedunculata,Sedum sarmentosum and Nicotiana tabacum.Finally,phylogenetic analyses on 39 grape family species were performed based on 79 common protein-coding chloroplast genes,so as to reveal the phylogenetic relationship among different genera and species of Vitaceae.The main result were as follows:1.The complete chloroplast genome sequence of 11 species of Vitis were determined and annotated.The chloroplast genomes of Vitis were highly conserved,of which sizes range from 160935 bp to 160982 bp.They all exhibited a typical quadripartite structure with a large single copy region(LSC,from 89159 bp to 89193bp),a small single copy region(SSC,from 19045 bp to 19073bp)and a pair of inverted repeats(IRs,from26250 bp to 26373bp).Each genome encodes 113 unique genes,comprising 79protein-coding genes,30 tRNA genes and 4 rRNA genes.In addition,two special genes ycf15 and ycf68,with no encoded protein correction-functions,annotated and located in invered repeat region.The guanine-cytosine contents of the chloroplast genome were very similar(37.4%).And the codon usage was biased towards A and T,particularly for the second and third position(61.61% and 69.74%).The statistical analysis of repetitive sequence and simple sequence repeats(SSR)was carried out to provide a basis for the related studies of genus Vitis.2.The results regarding comparison of 16 complete chloroplast genome sequences revealed that the two IR regions were more similar than the LSC and SSC regions.The chloroplast genomes in genus of Vitis were very conservative,and the Ampelopsis plastome with those chloroplast genomes of Vitis showed a high degree of synteny,as they all belong to the same family(Vitaceae).However,there were great differences between the other two species of angiosperm(Sedum sarmentosum and Nicotiana tabacum).The pairwise distance between 13 species of Vitis was closely linked with relative distance.The nucleotide diversity(Pi)of the coding and non-coding regions were analyzed separately across the 13 Vitis species,and ten sequences were determined with high degree of divergence,i.e.psbZ-trnG(UCC),csA-ndhD,atpF-atpH,accD-psaI,ndhF-rpl32,rps15-ycf1,trnK(UUU)-rps16,rpl32,rpl33 and atpF.Three of them were located in the coding region,while the rest were located in non-coding region.The results concerning comparison of the border positions showed that the size and distribution of rps19,ndhF,ycf1,?rps19 and?ycf1 were varying degrees of diversities and these differences reflect the evolution of chloroplast genome.3.Phylogenetic analysis of 39 species based on 79 common protein-coding chloroplast genes were carried out in order to evaluate the phylogenetic relationship among different genera and species of Vitaceae The ML and MP topologies from these analysis were consistent,five major monophyletic lineages,i.e.,the Vitis-Ampelocissus clade,the Parthenocissus-Yua clade,the core Cissus clade,the Cayratia-Cyphostemma-Tetrastigma clade and the Ampelopsis-Rhoicissus clade,were supported.Moreover,Vitis includes two described subgenera i.e.,subg.Muscadinia and subg.Vitis,as a monophyletic group.The subg.Vitis includes Eurasian lineage and New World lineage.