ArticleBMC genomics2009
Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- First EST-SSRs ofPlants (Basel, Switzerland) · 2025Article
- Polyphenolic composition, genetic profile and in vitro antioxidant and cytotoxic activities of artichoke varieties "Strunjanska articoka", "Romanesco" and "Violetto di Romagna".Scientific reports · 2025Article
- Genome-Wide Survey and Development of the First Microsatellite Markers Database (International journal of molecular sciences · 2022Article
- The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes.Frontiers in plant science · 2022Article
- Genetic diversity and population structure of Cynara cardunculus L. in southern Portugal.PloS one · 2021Article
- Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family.Molecular biology reports · 2018Article
- Genetic diversity and accession structure in European Cynara cardunculus collections.PloS one · 2017Article
- The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny.Scientific reports · 2016Article
- A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database.PloS one · 2016Article
- Rediscovering medicinal plants' potential with OMICS: microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties.Omics : a journal of integrative biology · 2014Article
- Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes.Frontiers in plant science · 2014Article
- Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex.BMC research notes · 2012Article
- RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.BMC genomics · 2012Article
- Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra.International journal of molecular sciences · 2012Article
- Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- In silico mining for simple sequence repeat loci in a pineapple expressed sequence tag database and cross-species amplification of EST-SSR markers across Bromeliaceae.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Identification of SNP and SSR markers in eggplant using RAD tag sequencing.BMC genomics · 2011Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers.
resultsA unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations.
conclusionEST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
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