Abstract: 【Objective】 A method was built to assemble complete chloroplast (cp) genome of Vitis and analyze its characteristics with Vitis vinifera cv. Cabernet Sauvignon, which will provide a methodological guidance for evolution and phylogenetic analysis of vitis in the future.【Method】Total genomic DNA was extracted from young leaves of Cabernet Sauvignon using plant genomic DNA kit. The small fragments (350 bp) of DNA libraries were constructed according to the manufacturer’s manual for the Illumina HiSeq PE150, and the sequencing depth was 10 fold. Grape cp reads were extracted by BLASTN software according to cp genome sequence of Arabidopsis thaliana (NC000932) and Pinot Noir (DQ424856). SOAPdenovo 2.04 assembled the extracted cp reads into complete chloroplast genome of Cabernet Sauvignon. Then its basic characteristics were analyzed using some bioinformatic softwares. 【Result】 This research obtained total of 5.2 G raw data after high-throughput sequencing. Among them, 0.42 G clean data of grape cp reads were extracted, and it accounted for about 8%. These extracted grape cp reads assembled the complete cp genome successfully. The characteristic analysis of grape cp genome showed that it was a circular molecule of 160 676 bp in length with a typical quadripartite structure, including a pair of inverted repeats (IRA and IRB) of 26 235 bp that were separated by large and small single copy regions (LSC and SSC) of 89 134 bp and 19 072 bp, respectively. A total of 154 predicted genes, including 99 protein-coding genes, 47 tRNA genes and 8 rRNA genes were identified. And the GC content of cp genome was 37.43%. Furthermore, the cp genome of Cabernet Sauvignon contained 37 tandem repeat sequences and 53 dispersed repeats. The length of most tandem repeat sequences was 11-42 bp. They accounted for 0.83% of whole cp genome, and the dispersed repeats accounted for 5.33%. Additionally, fifty short simple repeats (SSRs) loci of cp genome were detected. And most SSR loci were composed of A or T contributing to an obvious bias in base composition. Distribution of cp SSRs was non-uniform because the regions of LSC, SSC, and IR were located by 39, 7, and 4 SSRs, respectively. The codon usage of protein-coding genes was biased to use A/T bases. And among these codons, leucine (L) and cysteine (C) were the most and least used amino acids, respectively. The phylogenetic analysis showed that Cabernet Sauvignon had a closer genetic relationship with Pinot Noir, V. aestivalis and V. rotundifolia.【Conclusion】Based on high-throughput sequencing, the complete cp genome of Cabernet Sauvignon was obtained successfully. Cp and cpDNA were not required to isolate and extract in this method which shortened the experiment time, reduced the labor intensity and improved the feasibility. The subsequent characteristic analysis showed that gene structure, gene order, GC content and codon usage were identical with typical angiosperm. This research provided perfect and detailed data for the study of cp genome of Vitis vinifera, which also supplemented many deficiencies of characteristic analysis of cp genome of Vitis, such as repeat sequences, codon bias and SSRs.

Key words: cabernet sauvignon, chloroplast genome, high-throughput sequencing, characteristic analysis, phylogenetic analysis