title: Comparative Characterization of the Leaf Tissue ofPhysalis alkekengiandPhysalis peruvianaUsing RNA-seq and Metabolite Profiling.
abstract: The genusPhysalisin theSolanaceaefamily contains several species of benefit to humans. Examples includeP. alkekengi(Chinese-lantern plant, hôzuki in Japanese) used for medicinal and for decorative purposes, andP. peruviana, also known as Cape gooseberry, which bears an edible, vitamin-rich fruit. Members of thePhysalisgenus 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 thede novoassembly of the transcriptome from leaves ofP. alkekengiandP. peruvianausing Illumina RNA-seq technologies. We identified 75,221 unigenes inP. alkekengiand 54,513 inP. 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 inP. alkekengiandP. peruviana. To measure the variability of the withanolides including physalins and provide insights into their chemical diversity inPhysalis, we also analyzed the metabolite content in leaves ofP. alkekengiandP. peruvianaat 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 inPhysalisand 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 ofPhysalisspecies.
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Fukushima
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University Chiba, Japan.
authors.forename: Michimi
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Department of Biotechnology Research, Kazusa DNA Research Institute Chiba, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University Chiba, Japan.
authors.forename: Mami
authors.initials: M
authors.lastname: Yamazaki
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Eva
authors.initials: E
authors.lastname: Knoch
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Mori
authors.affiliation: RIKEN Center for Sustainable Resource Science Yokohama, Japan.
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Umemoto
authors.affiliation: Synthetic Organic Chemistry Laboratory, RIKEN Saitama, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Morita
authors.affiliation: Synthetic Organic Chemistry Laboratory, RIKENSaitama, Japan; RIKEN Center for Sustainable Resource ScienceSaitama, Japan.
authors.forename: Go
authors.initials: G
authors.lastname: Hirai
authors.affiliation: Synthetic Organic Chemistry Laboratory, RIKENSaitama, Japan; RIKEN Center for Sustainable Resource ScienceSaitama, Japan.
authors.forename: Mikiko
authors.initials: M
authors.lastname: Sodeoka
authors.affiliation: RIKEN Center for Sustainable Resource ScienceYokohama, Japan; Graduate School of Pharmaceutical Sciences, Chiba UniversityChiba, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
keywords: Physalis; de novo transcriptome assembly; deep sequencing; marker development; physalin; secondary metabolism; withanolide