Microsatellite markers for the bushy matgrass (Lippia alba) and related Lippia species

Lippia alba (Mill.) NE Brown (Verbenaceae) is a native species from South America that exhibits remarkable genetic and phenotypic variation. Four ploidal levels were described. To understand the relationships among the ploidal levels as well as the origins and evolution of the L. alba complex we sought to increase the number of available simple sequence repeat (SSR) markers. We performed a low-coverage (~2-fold) genomic DNA sequencing of a diploid accession and generated a de novo assembly. In order to enrich for SSRs in non-repetitive parts of the genome, reads were only screened for SSRs if they could not be mapped to the genome assembly. Fifty SSR markers were identified of which thirteen were selected for testing in 20 L. alba tetraploid accessions and in 12 other Lippia species. These markers were successfully amplified in related species with 85% average transferability. Thus, we demonstrate the utility of including a de novo assembly step to obtain SSR markers from low-coverage genomic datasets.