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Genomics

  • Davide Scaglione
  • Alberto AcquadroEmail author
  • Ezio Portis
  • Sergio Lanteri
Chapter
Part of the Compendium of Plant Genomes book series (CPG)

Abstract

A first assembly of globe artichoke genome was released in 2016 and the project required the adoption of a set of strategies to overcome the lack of a homozygous reference genotype. Moreover, the inability to exploit standard genotyping methods, normally adopted in inbred species where homozygous segregating progenies can be more easily obtained, posed some challenges. A low-pass genotyping-by-sequencing strategy for heterozygous individuals was implemented for the first time and required the development of dedicated tools. The method allowed to leverage very low coverage to impute genotypic states of F1 segregating individuals and use this information to arrange scaffolds in pseudomolecules. The availability of a chromosome-scale reference sequence allowed to depict, for the first time, the genomic landscape of globe artichoke. The work shed lights on its genes, their structure and function, orthology and synteny with other species, repeats and the timing of their expansion, age of speciation and whole-genome duplications. All the features revealed in this study expanded the knowledge base for comparative genomics across all plants. More importantly, the genome sequence of globe artichoke will facilitate transferability of genomic and genetic findings in the Compositae family, hence accelerating the discovery of the molecular mechanism at the base of economically important traits and their exploitation for selection, genetic engineering or utilization in biotechnological processes, in the light of the richness of nutraceutical properties of this species and its overall economic importance for the Mediterranean horticulture.

Keywords

Artichoke Genome Sequencing Gene prediction Age of speciation Genotyping Pseudomolecule 

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Davide Scaglione
    • 1
  • Alberto Acquadro
    • 2
    Email author
  • Ezio Portis
    • 2
  • Sergio Lanteri
    • 2
  1. 1.IGA Technology ServicesUdineItaly
  2. 2.DISAFA Plant Genetics and BreedingUniversity of TorinoGrugliasco, TorinoItaly

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