title: The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny.
abstract: Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. 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. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically important genes from related species.
authors.affiliation: DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.|The Genome Center, University of California, Davis, CA, USA.
authors.forename: Davide
authors.initials: D
authors.lastname: Scaglione
authors.affiliation: The Genome Center, University of California, Davis, CA, USA.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Reyes-Chin-Wo
authors.affiliation: DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Acquadro
authors.affiliation: The Genome Center, University of California, Davis, CA, USA.
authors.forename: Lutz
authors.initials: L
authors.lastname: Froenicke
authors.affiliation: DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
authors.forename: Ezio
authors.initials: E
authors.lastname: Portis
authors.affiliation: The Genome Center, University of California, Davis, CA, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Beitel
authors.affiliation: DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Tirone
authors.affiliation: Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, Catania, Italy.
authors.forename: Rosario
authors.initials: R
authors.lastname: Mauro
authors.affiliation: Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, Catania, Italy.
authors.forename: Antonino
authors.initials: A
authors.lastname: Lo Monaco
authors.affiliation: Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), University of Catania, Catania, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Mauromicale
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Fiorenzuola d'Arda, Italy.
authors.forename: Primetta
authors.initials: P
authors.lastname: Faccioli
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Fiorenzuola d'Arda, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
authors.affiliation: University of British Columbia, Vancouver, BC, Canada.
authors.forename: Loren
authors.initials: L
authors.lastname: Rieseberg
authors.affiliation: The Genome Center, University of California, Davis, CA, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Michelmore
authors.affiliation: DISAFA, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Lanteri
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D031943:Cynara scolymus / Q000235:genetics*; D004276:DNA, Satellite; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004276:DNA, Satellite; D035683:MicroRNAs