The grapevine (Vitis vinifera L.) is one of the most important fruit crops because of its economic value and cultural importance. It is also extremely diverse, with thousands of cultivars grown commercially worldwide. To elucidate the phylogenetic relationships of these cultivars, chloroplast DNA (cpDNA) sequences are oftenvery informative. Using the Ion Proton platform for non-targeted high-throughput whole genomic DNA sequencing, we determined the cpDNA sequences of 409 samples of vine cultivar from Slovenia and several other European countries. By using bioinformatics tools, we determined 93 single nucleotide variants and 102 unique cpDNA sequences. Haplotype analysis revealed that the cpDNA genotypes were dependent on their geographical origin. Since sequencing libraries were constructed using a non-conventional approach we validated the results by targeted sequencing of cpDNA regions containing 24 cpDNA SNP markers and subsequently compared variant data for these markers. A small number of discrepancies were found between the two approaches, which can be attributed to the parameters used in the data analysis pipeline.
|
