de novo characterization of the root transcriptome and development of est-ssr markers in paris polyphylla smith var. yunnanensis, an endangered medical plant

paris polyphylla smith var. yunnanensis (liliaceae) is an important traditional medicinal plant of the yunnan province in china. however, the genomic information regarding this plant is limited. to further understand its molecular background, we conducted illumina hiseq 2000 second-generation sequencing of this plant species. approximately 30,198,679 reads with an average length of 202 bases were obtained from its root cells. these reads were assembled into 56,095 unique sequences and approximately 49.7% of the unique sequences were annotated by basic local alignment search tool (blast) similarity searches against public sequence databases. most of these unigenes were mapped to carbohydrate metabolism, energy metabolism, and secondary metabolite biosynthetic pathways. additionally, 3,853 est-ssrs were identified as potential molecular markers in our unigenes. of these, 9 nuclear ssr markers were employed to assess genetic diversity and structure of 11 geographically disjunct populations. the present study revealed a moderate genetic diversity (he= 0.527) and low genetic differentiation (fst= 0.103), which may be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. the 11 studied populations were divided into two clusters based on the upgma dendrogram, which were not congruent with their geographical distributions. overall, the root transcriptome sequences generated in this study reveal novel gene expression profiles and offer important clues for further study of the molecular mechanism of paris’ root secondary metabolite synthesis and population genetics. the est-ssr markers identified will also facilitate marker-assisted selection in paris breeding.