Abstract
The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (Helianthus annuus) and horseweed (Conyza canadensis)) included in the study. Finally, a database, called “Cynara cardunculus MicroSatellite DataBase” (CyMSatDB) was developed to provide a searchable interface to the SSR data. CyMSatDB facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic vs genic context, perfect vs imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates.
Highlights
Introduction(2n = 2x = 34) is native to the Mediterranean Basin and includes the three fully cross-compatible taxa designated as the globe artichoke
The allogamous Asteraceae species Cynara cardunculus L. (2n = 2x = 34) is native to the Mediterranean Basin and includes the three fully cross-compatible taxa designated as the globe artichoke, the cultivated cardoon and the wild cardoon; the latter is assumed to be the ancestor of the former two cultivated forms [1, 2]
The most recent and extensive set of globe artichoke microsatellite was developed by Scaglione et al [12]; over 4,000 potential simple sequence repeat (SSR) loci were identified from expressed sequence tags (EST) and sample of them showed to be polymorphic among the parents of two mapping populations
Summary
(2n = 2x = 34) is native to the Mediterranean Basin and includes the three fully cross-compatible taxa designated as the globe artichoke Globe artichoke is grown for its edible immature inflorescences, while cultivated cardoon is cultivated mainly for its edible fleshy stems. Most of the world's production of globe artichoke is centered around the Mediterranean Basin, especially Italy [3]. The species was probably domesticated in Italy, where the most diverse primary genepool remains. Over 100 varieties are cultivated: they are generally classified on the basis of harvest time (early vs late) and/or inflorescence type (size, shape, presence/absence of spines, pigmentation of the outer bracts). While seed-propagated varieties and F1 hybrids are growing in popularity, vegetatively propagated planting material is still widely used, by producers of local varietal types
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