The first reference genome sequence of the highly heterozygous globe artichoke has been recently released (January 2016, www.artichokegenome.unito.it), organized in 17 pseudomolecules and including about 27,000 predicted genes. Since the release of the first genome draft, it was clear that, due to the its homozygous profile, the plant selected for the draft assembly should be flaked by other assembled genomes cultivated and highly heterozygous. Acquadro and colleagues (Sci Rep 7:5617, 2017) resequenced and assembled six Cynara cardunculus genotypes (40×), which are representative of the four main varietal types, as well as one genotype of cultivated cardoon (C. cardunculus var. altilis). The genomes were annotated revealing an analogous number of genes in all the genotypes, ranging from 27,121 in the ‘Catanese’ to 28,029 in the ‘Romanesco.’ The five proteomes were also analyzed/categorized for RGA features. A total of ~23.5 M SNPs/indels were discovered, and a functional SNPs analysis was established. Recently, to improve the quality metrics of the first reference genome assembly (v1.0), a resequencing of the genotype was attempted through the implementation of a Hi-C library and the production of a v2.0 of the assembly with improved assembly metrics. This new high-quality reference genome, together with the genomic data from the other resequenced genotypes, representing a one-stop resource for C. cardunculus genomics will enable map-based cloning of useful genes from the species and will enhance the taxonomic breadth of the data available for comparative plant genomics in Compositae.
Genome Resequencing
Alberto Acquadro;Lorenzo Barchi;Ezio Portis;Sergio Lanteri
2019-01-01
Abstract
The first reference genome sequence of the highly heterozygous globe artichoke has been recently released (January 2016, www.artichokegenome.unito.it), organized in 17 pseudomolecules and including about 27,000 predicted genes. Since the release of the first genome draft, it was clear that, due to the its homozygous profile, the plant selected for the draft assembly should be flaked by other assembled genomes cultivated and highly heterozygous. Acquadro and colleagues (Sci Rep 7:5617, 2017) resequenced and assembled six Cynara cardunculus genotypes (40×), which are representative of the four main varietal types, as well as one genotype of cultivated cardoon (C. cardunculus var. altilis). The genomes were annotated revealing an analogous number of genes in all the genotypes, ranging from 27,121 in the ‘Catanese’ to 28,029 in the ‘Romanesco.’ The five proteomes were also analyzed/categorized for RGA features. A total of ~23.5 M SNPs/indels were discovered, and a functional SNPs analysis was established. Recently, to improve the quality metrics of the first reference genome assembly (v1.0), a resequencing of the genotype was attempted through the implementation of a Hi-C library and the production of a v2.0 of the assembly with improved assembly metrics. This new high-quality reference genome, together with the genomic data from the other resequenced genotypes, representing a one-stop resource for C. cardunculus genomics will enable map-based cloning of useful genes from the species and will enhance the taxonomic breadth of the data available for comparative plant genomics in Compositae.
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