CyMSatDB: The Globe Artichoke (Cynara cardunculus var. scolymus) Microsatellite Database

The first high-quality genome assembly of the globe artichoke (Cynara cardunculus var. scolymus) has been recently produced at the DISAFA (Plant Genetics and Breeding) within the Compositae Genome Project (Scaglione et al. 2014, XXII PAG Conference). The assembly contains 13K scaffolds (N50= 125 Kbp), which represent 725 Mb of genomic sequence. Scaffolds were genetically anchored using a low-coverage genotyping by sequencing (GBS) of a mapping population and 17 pseudomolecules reconstructed. Peudomolecules as well as unmapped scaffolds were used for the bulk mining of SSR markers and for the construction of the first microsatellite marker database CyMSatDB (Cynara cardunculusMicroSatellite DataBase). Both perfect and compound SSRs were in-silico mined using the SciRoKo SSR-search module (http://kofler.or.at/bioinformatics/SciRoKo). On the whole, about 295,000 SSR motifs were identified which also include 66.700 compound SSRs.

CyMSatDB (http://www.artichokegenome.unito.it) is a user-friendly and freely accessible tool, and offers chromosome wise as well as location wise search of primers by implementing Primer3. This web application, based on a LAMP solution stack, organizes microsatellites data in a MySQL database and provides an effective and responsive interface developed in PHP. To cater the customized needs of wet lab, features with a novelty of an automated primer designing tool is added. The feature of user defined primer designing has great advantage in terms of precise selection from each chromosome, defined location, size of amplicons for ease of rapid genotyping. From our large marker dataset, the identification of markers with thermodynamic compatibility for multiplex designing can be also accomplished.