Characterization and cross-species transferability of EST–SSR markers developed from the transcriptome of Dysosma versipellis (Berberidaceae) and their application to population genetic studies

Abstract

Dysosma (Berberidaceae), which comprises seven herbaceous perennial species, has long been used as main sources of a traditional Chinese medicine, “Guijiu.” Despite its ecological and economic importance, molecular research of Dysosma has lagged behind because of the shortcoming of molecular markers. In this study, a cDNA library of D. versipellis leaves was sequenced using the Illumina HiSeq™ 2000 sequencing system. A total of 44,855 nonredundant unigenes were assembled from 57.6 million reads, and 5,167 expressed sequence tag–simple sequence repeats (EST–SSRs) were identified in 4,536 unigenes. Trinucleotide motifs were the most common type, with a frequency of 43.7 % (2,260). Among the 5,167 EST–SSRs, 1,050 primer pairs were successfully designed. After selecting 80 of these pairs at random for further validation, 19 pairs were identified as true-to-type SSR loci, and 14 of those could reliably amplify polymorphic bands from 12 individuals of D. versipellis. These 14 EST–SSR markers showed high average genetic diversity (e.g., NA = 6.29; HE = 0.528), when surveyed across four D. versipellis populations, and were also transferable to almost all other Dysosma species, excepting one marker (four instead of six species). Finally, 11 polymorphic markers were chosen to provide insights into the population structure of D. versipellis and its presumed sister species, D. pleiantha. Both genetic distance and structure analyses identified two genetic clusters largely congruent with the current species classification. These findings indicate that the EST–SSRs examined can be used with confidence in future population genetic studies of both D. versipellis and D. pleiantha.