系统发生学与进化生物学杂志

Comparative Bioinformatics Analyses of the Chloroplast Genomes of Vitis vinifera with Two Caucasica Subspecies of Grape Fruit

Abstract

F. Talat, S. Shahdparvar and M. Badri Anarjan

Grape (Vitis vinifera) is a genus of tree in the family of Vitaceae. V. vinifera's species belong to Eurasian grapes. The genome of chloroplast is the most comprehensive genome in plants, and it has many features for evolution analyses due to the unique molecular structure and single-parent inheritance. The goals of this research were study and compare of the complete sequences chloroplast genomes of Saperavi and Meskhuri mtsvane from Caucasia subspecies with common grape (Vitis vinifera), as well as genomes structure analysis, gene content, organization and repetitive sequences, codon usage and comparison among genomes. The chloroplast genome of Vitis vinifera is a circular DNA molecule with 160928 base pairs (bp), which is longer than the chloroplast genomes of Saperavi and Meskhuri mtsvane varieties. The large and small unique regions are separated by two inverted repeat regions a, b. In three genomes, the complete genome contains 131 genes, which include 79 protein coding genes, 4 rRNA genes and 30 tRNA genes. In other words, there are totally 113 single-copy genes and 18 double-copy genes located in inverted repeat region (IR) in the three studied genomes. The SSRs of the chloroplast genomes were identified and the results indicated that the chloroplast genomes of Vitis vinifera and Saperavi both have 74 SSRs and Meskhuri mtsvane has 73 SSRs. The chloroplast SSRs are important and useful for genetic diversity studies. Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair.