Data from: Development of chloroplast genomic resources for Cynara

In the present work, high-throughput sequencing technologies were used to develop the first chloroplast (cp) resources for the Cynara genus along the whole cp genome of 20 genotypes. Our panel includes seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera, and C. syriaca). Primer pairs for long range PCR in Cynara are provided. A de novo assembly strategy, combined with a reference based assembly allowed to reconstruct each cp genome. Multiple sequence alignments with the newly sequenced genotypes and two additional Cynara cp genomes retrieved from NCBI database revealed 126 parsimony informative characters and 258 singletons in Cynara for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSRs were designed and markers were validated in Cynara. Phylogenetic analysis based on the whole cp genome provided a better resolution compared to the analysis established only on parsimony informative characters. Therefore, the complete cp sequence can be considered a valuable marker for studying relationships within this genus and as a super-barcode in plants.