Resequencing of Cynara cardunculus.. genotypes and detection of chromosome-scale single nucleotide polymorphisms (SNPs)/indels

摘要

Cynara cardunculus L. (family Asteraceae, a.k.a. Compositae; 2n=2x=34) is an outcrossing species that includes three fully cross-compatible botanical taxa: globe artichoke (var. scolymus (L.) Fiori), cultivated cardoon (var. altilis D.C.) and their common ancestor wild cardoon (var. sylvestris (Lam.) Fiori). Recently, we published the sequence of the globe artichoke genome (http://www.artichokegenome.unito.it), which covers 725 Mb of the estimated genome size of 1084 Mb and encodes 26,889 predicted genes. Here we report on Ulumina re-sequencing of globe artichoke and cultivated cardoon genotypes at a coverage of about 48x and 43x, respectively, as well as a low coverage (0.5-lx) genotyping-by-sequencing of 163 of their Fi progeny. Linkage analysis of the segregant population, based on a two-way pseudo-testcross approach, resulted in 73% of the assembled genome being anchored along 17 chromosomal pseudo-molecules, corresponding to the haploid chromosome number of the species. We also performed 35-fold Ulumina resequencing of four globe artichoke genotypes, which are representative of the core varietal types in cultivation, as well as a genotype of the related taxon, cultivated cardoon. The five genomes were reconstructed at a chromosomal scale andstructurally annotated. Gene prediction highlighted an analogous number of genes. On the whole, ~23.5 million single nucleotide polymorphisms (SNPs)/indels were discovered, which represent key tools to dissect the path from sequence variation to phenotype as well as for designing diagnostic markers.