Plastid genomics of Vitis vinifera L. for understanding the molecular basis of  grapevine (Vitis vinifera L.) domestication

Abstract

Over the past decade, numerous scientific studies have utilized advanced next-generation plastid DNA technologies to assess the genetic diversity of grapevine (Vitis vinifera L.) worldwide, aiming for a deeper understanding the possible molecular mechanisms of domestication process. For such studies, it is essential to include both cultivated varieties (Vitis vinifera subsp. vinifera) and their wild ancestors (Vitis vinifera subsp. sylvestris) from all potential distribution and domestication sites, as only by comparing the genetic profiles of cultivated and wild specimens can the potential sites of domestication be identified. The main goal of the presented research was the next-generation sequencing (NGS) of complete plastid genomes mainly from European and Mediterranean wild grapevines, as well as cultivated varieties from Europe and Georgia (South Caucasus), and American and Asian Vitis species, followed by in silico genome assembly and phylogenetic analyses. The results revealed that plastomes of European and Mediterranean wild grapevines predominantly exhibit the so-called GTA haplotype; Portuguese wild grapevines exhibit a new type of ATA plastid haplotype; Plastomes of Asian and American species are distinct from those of European and Mediterranean grapevines and the Rkatsiteli haplotype (AAA) remains genetically unique among the plastomes sequenced to date.