Cynara cardunculus is a member of the Asteraceae family which is important, in particular the globe artichoke, for the Mediterranean basin economic stability giving employment for the whole year round. It is also a valuable source of biopharmaceutical compounds and exploitable as a source of lignocellulosic biomass and seed oil suitable for both edible and bio-fuel end-uses. The existing reference C. cardunculus genetic map consists of about 1,000 informative markers assembled into 17 major linkage groups. To further saturate the maps of the species a wide set of both genomic and transcriptomic SNPs (single nucleotide polymorphism) were obtained through the exploitation of NGS (next generation sequencing) technologies following two distinct schemes. The first one, targeting the nuclear genome, was carried out by Illumina sequencing of RAD (restriction associated DNA) tags of three mapping parents and generated a total of ~19.000 genomic contigs (mean 312 bp) and ~17.000 SNPs (density 1/139 bp). The second one, targeting the transcriptome, was conducted by 454 sequencing of the same mapping parents. Raw data were de novo assembled and annotated to generate the first reference transcriptome of the species (38,726 unigenes, 32.7 Mbp). Afterwards, the 454 reads, together with Illumina paired-ends from other eight C. cardunculus genotypes were aligned on the reference contig set and ~195.000 SNPs were called (density 1/169 bp in coding regions). These SNPs represent a one-stop resource to produce a dense C. cardunculus genetic map via high-throughput genotyping technologies.
Genomics of Cynara cardunculus through the exploitation of NGS technologies
ACQUADRO, Alberto;PORTIS, Ezio;SCAGLIONE, DAVIDE;LANTERI, Sergio
2016-01-01
Abstract
Cynara cardunculus is a member of the Asteraceae family which is important, in particular the globe artichoke, for the Mediterranean basin economic stability giving employment for the whole year round. It is also a valuable source of biopharmaceutical compounds and exploitable as a source of lignocellulosic biomass and seed oil suitable for both edible and bio-fuel end-uses. The existing reference C. cardunculus genetic map consists of about 1,000 informative markers assembled into 17 major linkage groups. To further saturate the maps of the species a wide set of both genomic and transcriptomic SNPs (single nucleotide polymorphism) were obtained through the exploitation of NGS (next generation sequencing) technologies following two distinct schemes. The first one, targeting the nuclear genome, was carried out by Illumina sequencing of RAD (restriction associated DNA) tags of three mapping parents and generated a total of ~19.000 genomic contigs (mean 312 bp) and ~17.000 SNPs (density 1/139 bp). The second one, targeting the transcriptome, was conducted by 454 sequencing of the same mapping parents. Raw data were de novo assembled and annotated to generate the first reference transcriptome of the species (38,726 unigenes, 32.7 Mbp). Afterwards, the 454 reads, together with Illumina paired-ends from other eight C. cardunculus genotypes were aligned on the reference contig set and ~195.000 SNPs were called (density 1/169 bp in coding regions). These SNPs represent a one-stop resource to produce a dense C. cardunculus genetic map via high-throughput genotyping technologies.
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