L. Wang - Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, ۶۵۰۲۰۱, People’s Republic of China.
Y. Yang - China Tobacco Yunnan Industrial Co., Ltd, Kunming ۶۵۰۲۰۱. People’s Republic of China.
Y. Zhao - China Tobacco Yunnan Industrial Co., Ltd, Kunming ۶۵۰۲۰۱. People’s Republic of China.
S. Yang - Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, ۶۵۰۲۰۱, People’s Republic of China.
S. Udikeri - University of Agricultural Sciences, Dharwad, Pin-۵۸۰۰۰۵, Karnataka, India.
T. Liu - Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, ۶۵۰۲۰۱, People’s Republic of China.

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 ۲۰۰۰ second-generation sequencing of this plant species. Approximately ۳۰,۱۹۸,۶۷۹ reads with an average length of ۲۰۲ bases were obtained from its root cells. These reads were assembled into ۵۶,۰۹۵ unique sequences and approximately ۴۹.۷% 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, ۳,۸۵۳ EST-SSRs were identified as potential molecular markers in our unigenes. Of these, ۹ nuclear SSR markers were employed to assess genetic diversity and structure of ۱۱ geographically disjunct populations. The present study revealed a moderate genetic diversity (He= ۰.۵۲۷) and low genetic differentiation (Fst= ۰.۱۰۳), which may be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. The ۱۱ 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.

HiSeq second-generation sequence, Saponin, Simple sequence repeat