The complete chloroplast genome sequence of Vitis vinifera ‘Krasnostop Zolotovskiy’, an autochthonous variety of the Don Valley

Abstract

DNA sequence data from complete chloroplast genomes expand our understanding of plant diversity and contributes to our understanding of evolutionary relationships among species. De novo assembly and annotation of plant chloroplast genomes are difficult due to the high number of repeats and low number of plant chloroplast genomes in international databases. The development of long-read sequencing platforms such as PacBio and Oxford Nanopore, as well as specialized assemblers, is simplifying the process of assembling and annotating large circular molecules. In this work, we report the complete chloroplast genome of the autochthonous Vitis vinifera variety ‘Krasnostop Zolotovskiy’, obtained de novo by the hybrid assembly method using short and long DNA reads. The circular genome of the chloroplast is 160,927 bp long with a GC ratio of 37.38 %. It has four subregions: large single-copy (LSC) region of 71,946 bp, a small single-copy (SSC) region of 36,273 bp, and two inverted repeat regions (IRs) of 26,354 bp each. The chloroplast genome of V. vinifera ‘Krasnostop Zolotovskiy’ harbours 129 genes, comprising 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. We also carry out a phylogenetic analysis based on all the complete sequences of grape chloroplast genomes available in the databases, which shows that the V. vinifera ‘Krasnostop Zolotovskiy’ does not have a direct origin with any European variety.