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The genus  Physalis  in the  Solanaceae  family contains several species of benefit to humans. Examples include  P. alkekengi  (Chinese-lantern plant, hôzuki in Japanese) used for medicinal and for decorative purposes, and  P. peruviana , also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of the  Physalis  genus are a valuable resource for phytochemicals needed for the development of medicines and functional foods. To fully utilize the potential of these phytochemicals we need to understand their biosynthesis, and for this we need genomic data, especially comprehensive transcriptome datasets for gene discovery. We report the  de novo  assembly of the transcriptome from leaves of  P. alkekengi  and  P. peruviana  using Illumina RNA-seq technologies. We identified 75,221 unigenes in  P. alkekengi  and 54,513 in  P. peruviana . All unigenes were annotated with gene ontology (GO), Enzyme Commission (EC) numbers, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We classified unigenes encoding enzyme candidates putatively involved in the secondary metabolism and identified more than one unigenes for each step in terpenoid backbone- and steroid biosynthesis in  P. alkekengi  and  P. peruviana . To measure the variability of the withanolides including physalins and provide insights into their chemical diversity in  Physalis , we also analyzed the metabolite content in leaves of  P. alkekengi  and  P. peruviana  at five different developmental stages by liquid chromatography-mass spectrometry. We discuss that comprehensive transcriptome approaches within a family can yield a clue for gene discovery in  Physalis  and provide insights into their complex chemical diversity. The transcriptome information we submit here will serve as an important public resource for further studies of the specialized metabolism of  Physalis  species.

Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling