Molecular evolutionary studies of grape based on next-generation plastid and mitochondrial genomics

The complete chloroplast DNA sequence of V. aestivalis, V. amurensis, V. flexuosa and V. coignetiae was determined by Illuminia sequencing and compared with our previously sequenced Vitis vinifera cultivars and American grape species. The comparison of sequenced chloroplast DNA revealed presence of five long size indels in the plastid genome, which were most informative during the phylogenetic and phylogeographic analysis of different grape species. A 54-bp deletion in trnC-GCA-petN intergenic spacer was detected in three out of four haplogroups of Vitis vinifera. This deletion was absent among the members of Pinot-Ckhaveri haplogroup (GTA haplogroup) and also in the American and Asian species. Additionally 4 indels were revealed in the chloroplast DNA genome. The 33-bp duplication in rps16-trnQ-UUG intergenic spacer was observed in ATT, ATA, AAA haplogroup of Vitis vinifera and in the American and Asian species, 18-bp duplication in trnS-GCU-trnG-GCC intergenic spacer was observed in the ATT haplogroup and another 18-bp duplication in rpoC2 gene in the AAA haplogroup. The novel, 46-bp long deletion was found in trnD-GUC- trnY-GUA intergenic spacer of two Asian V. amurensis and V. flexuosa species. The complete mitochondrial DNA sequence analysis of Georgian cultivars also revealed a high level of identity among the members of the same haplogroup. Several long size indels were detected between the representatives of different haplogroups. A phylogenetic scheme based on the consequent order of indels in grape plastid DNA is presented.