The Chloroplast Genome

In the last years, the availability of chloroplast genomes for plants and algae is increasing. These data can be useful both in the biotechnological area and in the evolutionary field, for the analysis of phylogenetic relationships among groups of organisms. Thanks to the advance of high-throughput sequencing, it is now possible to obtain the chloroplast genome sequence as a contaminant of whole-genome sequencing projects. Otherwise, the entire organelle genome can be recovered by means of long-range PCR amplification, using universal primers designed on highly conserved regions. The fragments obtained can be massively sequenced and the reads mapped on a reference genome. The chloroplast genomes of the Cynara cardunculus taxa, namely the globe artichoke, wild and cultivated cardoon and of other Cynara wild species are now available in the public databases. The structure of the Cynara chloroplast genome shows the classical quadripartite organization, with a long- and a short-single copy region and two inverted repeats. Within the globe artichoke, a marked variation is observed between the Romaneschi group and the other artichoke varietal types, due to some deletion events present in the Romaneschi. The highly variable regions found in the chloroplast genome can be used for barcode applications and phylogenetic relationships, not only in the genus Cynara, but also in the Asteraceae family.