Comparative Analyses And Phylogenetic Relationships Of Complete Chloroplast Genomes From The Ampelopsideae(Vitaceae)

The Ampelopsideae plants in the Vitaceae family,including the genera of Ampelopsis,Nekemias,Rhoicissus,and Clematicissus,are commonly used as traditional Chinese herbal medicine due to their various medicinal properties such as clearing heat,detoxification,promoting blood circulation,activating collaterals,and relieving pain.However,these plants have some confusion in use due to factors such as plant morphology,regional medicinal practices,and homonyms.Traditional classification methods based on morphology and active substance detection can effectively differentiate between varieties with significant differences in characteristics.However,it is challenging to distinguish between closely related species with minor characteristic differences.Therefore,clarifying the systematic evolutionary relationship between species in this group is significant for the development and utilization of germplasm resources.In this study,we sequenced the genomes of 10 species in the Ampelopsideae using high-throughput sequencing technology,assembled complete chloroplast genomes using bioinformatics tools,annotated and compared the complete chloroplast genomes,developed molecular markers,and conducted a systematic phylogenetic analysis.This study will contribute to in-depth research on the systematic evolution of Ampelopsideae,help identify species in this genus,facilitate population genetics research,and provide basic data for the development and utilization of germplasm resources.The main research results are as follows:1.The chloroplast genome of Ampelopsideae plants had a typical tetrad structure,consisting of a large single copy region,a small single copy region and two reverse repeat regions.The length of the chloroplast genome was 160,600 ～163,016 bp,the GC content ranged from 37.2% to 37.6%,and could encoded 132 ～134 gene,including 87 common genes,37 tRNAs and 8 rRNAs,and 1～2pseudogenes in some species.The chloroplast genome sequence collinearity was complete,and no gene rearrangements or inversions occurred.The chloroplast genome of Nekemias showed obvious contraction and expansion at the IR/SC boundary.2.Gene evolution was species-specific.ccsA and rpl20 genes underwent positive selection in all species of Ampelopsideae,psaC and atpI genes were selected for evolution only in Rhoicissus digitata,rps14,rpl23,ycf2,and rpoC2 genes were selected for evolution only in the Nekemias,and ndhA,rps19,and rps8 genes were selected for evolution only in Ampelopsiss.3.Phylogenetic analysis showed that the Vitaceae could be divided into five evolutionary branches,namely,Ampelopsideae,Cisseae,Cayratieae,Parthenocisseae and Viteae.Ampelopsideae,the first evolutionary branch,included three genera:Ampelopsiss、Nekemias、and Rhoicissus.Phylogenetic analysis results supported the latest taxonomic results that Nekemias is a monophyletic independent,separated from the original Ampelopsiss.The differentiation time of Ampelopsideae is about 84.77 Ma to date(95% HPD,76.81-95.47 Mya).4.The evaluation of the applicability of international universal barcodes in Ampelopsideae revealed that the matK+rbcL+trnH-GUG-psbA combination was best identified up to 95% as expected for species identification.The trn H-GUGpasA 、 trnK-UUU-rps16 、 psbM-trnD-GUC 、 psbZ-trnG-GCC 、 trnT-UGU-trnLUAA、rpl33-rps18、clpP1 and rps19-rpl12 in the large single-copy region,and ndhF-rpl32,ndhGndhI and ycf1 in the small single-copy region of the chloroplast genome,are highly variable regions,could be used as DNA barcodes.