GC collaboration with Italian group on artichoke genome bears fruit

ocean-mist-castroville-ranch-980x360 A team of researchers led by Sergio Lanteri of the University of Torino in Italy and Richard Michelmore of the University of California, Davis, has sequenced the genome of Cynara cardunculus var. scolymus, the globe artichoke, a diploid with 34 chromosomes and a genome size of just over one billion base pairs. Italy is the global leader in artichoke cultivation, in 2013 producing 547,799 tons. In North America, California is responsible for 100% of the 42,865 tons produced here, with 80% coming from Monterey County, where the town of Castroville holds an annual festival in honour of the savoury thistle. Since the 1920s, the artichoke fields of the Pajaro Valley have developed into a crop worth $50 million each year. Michelmore, professor of plant pathology and Director of the Genome Center, is co-PI of the Compositae Genome Project, an international effort to sequence the genomes of this large and varied plant family, which includes lettuce, sunflower, safflower, calendula, wormwood, and chicory, in addition to both globe and Jerusalem artichoke. The globe artichoke genome assembly was generated using ~133-fold Illumina sequencing data and covers 725 of the 1,084 Mb genome. The sequence provides information on the overall organization and gene content, predicting 27,000 genes, along with structural and functional annotation. Furthermore, it is now possible to gather information on the timing of speciation, whole genome duplication and expansion of transposable elements or ‘jumping genes’. Thanks to the re-sequencing of globe artichoke and cultivated cardoon parental genotypes, and low-coverage genotyping-by-sequencing of their F1 progeny, the assembled genome was anchored along 17 chromosomal pseudomolecules, corresponding to the haploid chromosome number of the species. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. The understanding of the genome structure of globe artichoke is fundamental to the molecular deciphering of complex traits and will facilitate the identification of economically important genes from related species. The sequence was published in Scientific Reports (Nature Publishing Group) and is available at www.artichokegenome.unito.it and at NCBI: The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny