De Novo Characterization of the Root Transcriptome and Development of EST-SSR Markers in Paris polyphylla Smith var. yunnanensis, an Endangered Medical Plant

Abstract

Paris polyphylla Smith var. yunnanensi s (Liliaceae) is an important traditional medicinal plant of the Yunnan Province in China. Ho wever, the genomic information regarding this plant is limited. To further underst and its molecular background, we conducted Illumina HiSeq 2000 second-generation seq uencing of this plant species. Approximately 30,198,679 reads with an average leng th 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 an notated by Basic Local Alignment Search Tool (BLAST) similarity searches against pub lic sequence databases. Most of these unigenes were mapped to carbohydrate metaboli sm, energy metabolism, and secondary metabolite biosynthetic pathways. Additio nally, 3,853 EST-SSRs were identified as potential molecular markers in our un igenes. Of these, 9 nuclear SSR markers were employed to assess genetic diversity a nd 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 mo re continuous distribution. The 11 studied populations were divided into two clusters based on the UPGMA dendrogram, which were not congruent with their geographical di stributions. Overall, the root transcriptome sequences generated in this study rev eal novel gene expression profiles and offer important clues for further study of the mole cular mechanism of Paris ’ root secondary metabolite synthesis and population genet ics. The EST-SSR markers identified will also facilitate marker-assisted selection in Paris breeding. Keywords: HiSeq second-generation sequence, Saponin, Simple s equence repeat.