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ISHS Acta Horticulturae 1147: IX International Symposium on Artichoke, Cardoon and Their Wild Relatives

The chloroplast genome as a tool for exploring genetic relationships among globe artichoke, leafy cardoons and wild artichokes

Authors:   P.L. Curci, D. De Paola, G. Sonnante
Keywords:   Cynara, chloroplast complete sequence, high-throughput sequencing, informative regions, phylogenetic relationships
DOI:   10.17660/ActaHortic.2016.1147.9
Abstract:
The main aim of this work was to isolate the entire chloroplast (cp) genome sequences of Cynara taxa, in order to retrieve the most useful resources for phylogenetic and population studies. Twenty-two samples were analysed, of which 18 belonged to the three taxa of C. cardunculus L., and the remaining to four wild species (C. syriaca, C. cornigera, C. baetica, and C. humilis). First, we obtained reads by whole-genome and a BAC clone of the 'Brindisino' globe artichoke by means of high-throughput sequencing. This genome was assembled, its size was 152,529 bp and it consisted of two single-copy regions separated by a pair of inverted repeats of 25,155 bp. The large and the small single-copy regions spanned 83,578 and 18,641 bp, respectively. For the other genotypes, a long-range PCR approach was employed for producing partially overlapping amplicons. These fragments were high-throughput sequenced and reads were assembled for each genotype using de novo and reference-guided methods. No structural differences regarding gene content and order were highlighted among all analysed genotypes. A conserved structure was also observed among other eight Asteraceae species analysed. Cynara cp genome consists of 114 unique genes, including 30 tRNA, 4 rRNA, and 80 predicted protein-coding genes. The comparative analysis among all newly sequenced genomes allowed the discovery of a large number of informative loci, in terms of variable microsatellites, INDELS, and SNPs. The Cynara complete cp sequence allowed the placing of this genus in the Asteraceae family tree and, thanks to the set of samples considered helped clarify the phylogenetic relationships within this genus.

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