Abstract

The high-throughput technologies have helped promote sequencing of many plant genomes. This showed to be the fastest approach for developing molecular resources in agriculture and ecology and revolutioned the way in which the research products are generated. In the present work, 22 samples from Cynara L. genus were analysed, including 18 genotypes belonging to the three taxa of C. cardunculus L., along with other four wild species (C. syriaca, C. cornigera, C. baetica, and C. humilis).The main aim was to isolate the entire chloroplast (cp) genome sequences from this germplasm, in order to retrieve the most useful resources for phylogenetic and population studies in the Cynara genus. Firstly, reads obtained by whole-genome and BAC clone high-throughput sequencing of the "Brindisino" globe artichoke were used to assemble the cp genome. This genome sized 152529 bp and consisted of two single-copy regions separated by a pair of inverted repeats (IRs) of 25155 bp. The large (LSC) and the small (SSC) single-copy regions spanned 83578 bp and 18641 bp, respectively.For the other genotypes, a different approach was used. The Cynara cp genome was virtually divided into 15 regions and long-range PCR was employed for producing the same number of partially overlapping amplicons. Subsequently, all sets of amplicons were sequenced with an Illumina platform. Sequences were then assembled for each genotype using de novo and reference-guided methods. For reference-based assembly we used the cp sequence of cultivar "Brindisino" (KM035764) as a reference. No structural differences regarding gene content and order were highlighted among all analysed genotypes. 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. We developed a new set of primer pairs directed to the amplification of SSR markers, which could be used for exploring the diversity of Cynara populations. Furthermore, the Cynara complete cp sequence allowed the placing of this genus in the Asteraceae family tree.

Autore Pugliese

• Sonnante Gabriella

Tutti gli autori

• Curci P.L.; De Paola D.; Danzi D.; Sonnante G.

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Anno di pubblicazione

2015

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