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. 2017 Jul 17;7(1):5617.
doi: 10.1038/s41598-017-05085-7.

Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation

Alberto Acquadro  1 , Lorenzo Barchi  1 , Ezio Portis  2 , Giulio Mangino  1 , Danila Valentino  1 , Giovanni Mauromicale  3 , Sergio Lanteri  1
Affiliations

Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation

Alberto Acquadro et al. Sci Rep. .

Abstract

The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated. Gene prediction indicated a similar number of genes, while distinctive variations in miRNAs and resistance gene analogues (RGAs) were detected. Overall, 23,5 M SNP/indel were discovered (range 6,34 M -14,50 M). The impact of some missense SNPs on the biological functions of genes involved in the biosynthesis of phenylpropanoid and sesquiterpene lactone secondary metabolites was predicted. The identified variants contribute to infer on globe artichoke domestication of the different varietal types, and represent key tools for dissecting the path from sequence variation to phenotype. The new genomic sequences are fully searchable through independent Jbrowse interfaces (www.artichokegenome.unito.it), which allow the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for C. cardunculus genomics.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Feature content analysis in the sequenced genomes of C. cardunculus. (a) Heads of the six analyzed genotypes (REF, VT, SP, VS, A41, C3. (b) Relative number of predicted genes, miRNAs loci and total RGAs loci. (c) Distribution of orthologous gene families in 2 C (reference), VT, SP, VS, A41 and C3 genotypes, calculated using OrthoMCL.
Figure 2
Figure 2
RLP and RLK resistance genes dendrogram of the six C. cardunculus genotypes. Taxa missing one or more RGA gene from at least one genotype are highlighted in light blue; clusters with one or more duplicated genes in one genotype are highlighted in orange, while clusters with at least one gene missing from one genotype and also containing at least one duplicated gene from one genotype are highlighted in purple.
Figure 3
Figure 3
Representation of the existing genetic variability among the C. cardunculus genotypes analyzed. (a) Circos diagram depicting gene and heterozygous SNP densities; from the outer circle to the inner circle: A) Heat map of gene density in the reference genome; 1 M histograms representing the density of heterozygous SNPs for the Reference (track B) A41 (track C), SP (track D), VS (track E), C3 (track F), VT (track G). (b) UPGMA-based dendrograms of the six genotypes taking into account 23 M SNPs and (c) 500 k coding SNPs.
Figure 4
Figure 4
SNP categorization of coding and non-coding variants. SNP effect by type and region for homozygous (a) and heterozygous (b) regions. SNP effect by functional class for homozygous (c) and heterozygous (d) regions.
Figure 5
Figure 5
Coding SNPs data in CQAs and SLs pathways. (a) Number of genes, polymorphic genes, variants and high deleterious impact SNPs in CQA- (light blue) and SL- (orange) related genes. Phylogenetic trees of proteins belonging to CQA-related transferase genes from the six genotypes analyzed (b) and to SL-related p450 genes from the same accessions (c).
See this image and copyright information in PMC

References

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