A Phylogenetic Study Of Vitis Based On Chloroplast Genomes

Vitis contained about 70 species in the world.Due to the frequent interspecific hybridization and morphological variation,the classification of Vitis is always controversial.At present,there are relatively few studies on the evolution of the genus Vitis,while the domestic research is mostly in the form of morphology,and the research on molecular systematics is less.The chloroplast genome has unique value in studying the evolutionary relationship of plant systems.In this study,24 chloroplast genomes of 22 Vitis species assembled in the early stage of the laboratory were studied.First,a comparative analysis of the 24 chloroplast genomes(repeat sequences,contraction and expansion of IR region,genomic variation,codon bias,sequence differentiation)was analyzed.Secondly,using the chloroplast genome to reconstruct the phylogenetic relationship of Vitis.The main findings are as follows:1.The repeated sequences of 24 accessions showed that the repeats of Vitis were mostly distributed in the non-coding region of the chloroplast genome,and the number of repeats between different species did not change much;The contraction and expansion of the IR region illustrated that the ycf1 pseudogene of most Chinese wild grape chloroplasts was 0 bp from the JSA border,while the ycf1 pseudogene of North American wild grapes was about 20 bp from the JSA border,indicating that compared with wild grapes in North America,the IR sequence of the Chinese wild grapes chloroplast genomes was significantly contracted;After removing the IRB region of the chloroplast genome,2238 mutation sites were detected from the chloroplast genome of the other 23 Vitis accessions,including 1817 SNP sites and 421 INDEL sites(245 inserts and 176 deletions).These variant hotspots can be used as potential molecular markers for the identification of Vitis germplasm resources;A study of the preference analysis of codon codons shows that the Vitis chloroplast genome codon is similar to most angiosperms and preferably ends with AT;Sequence differentiation analysis showed that the sequence differentiation in the genus Vitis was low.According to the K2 p genetic distance analysis,the Subgens Muscadinia and the Subgens Euvitis could be effectively distinguished,while a certain difference in genetic distance between the North American wild grapes and Chinese wild grapes was also existed.2.The phylogenetic study of Vitis was carried out based on the chloroplast LSC+SSC+IR sequence using ML method and BI method.The results showed that the genus Vitis can be divided into Subgens Euvitis and Subgens Muscadinia,and Subgens Euvitis include East Asian,Eurasian and North American populations,which was consistant with traditional classification.Chinese wild grapes can be further divided into 4 subclades.Subclade I included Vitis davidii.Subclade II consisted of Vitis pseudoreticulata and Vitis hancockii.Subclade III consisted of Vitis piasezkii,Vitis sinocinerea,Vitis ficifolia,Vitis bryoniifolia,Vitis tsoii and Vitis ruyuanensis.Subclade IV is composed of Vitis coignetiae and 11 Chinese wild grapes;The differentiation time of Vitis was studied using BEAST software.3.The differentiation time of Vitis was estimed at 44.3 Ma(95% HPD: 32.4-66.7 Ma),The differentiation time of Eurasian branch of Vitis was estimated to have occurred at 27.9 Ma(95% HPD: 19.9-34.1).The differentiation time of Chinese wild grapes was estimed at 20.8M(95% HPD: 13.7-27.7Ma).