Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex

The vase tunicate, Ciona intestinalis species complex, has become a good model for ecological and evolutionary studies, especially those focusing on microevolution associated with rapidly changing environments. However, genome-wide genetic markers are still lacking. Here we characterized a large set of genome-wide gene-associated microsatellite markers for C. intestinalis spA (= C. robusta). Bioinformatic analysis identified 4654 microsatellites from expressed sequence tags (ESTs), 2126 of which successfully assigned to chromosomes were selected for further analysis. Based on the distribution evenness on chromosomes, function annotation and suitability for primer design, we chose 545 candidate microsatellites for further characterization. After amplification validation and variation assessment, 218 loci were polymorphic in at least one of the two populations collected from the coast of Arenys de Mar, Spain (N = 24 - 48) and Cape Town, South Africa (N = 24 - 33). The number of alleles, o...