SE173:/S01/M01/D01

Sample Set Information

ID	TSE1331
Title	Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling
Description	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.
Authors	Fukushima, A., Nakamura, M., Suzuki, H., Yamazaki, M., Knoch, E., Mori, T., Umemoto, N., Morita, M., Hirai, G., Sodeoka, M. and Saito, K.
Reference	Front Plant Sci. 2016 Dec 20;7:1883. doi: 10.3389/fpls.2016.01883
Comment

PubMed

Sample Information

ID	S01
Title	Physalis alkekengi var. franchetii
Organism - Scientific Name	Physalis alkekengi var. franchetii
Organism - ID	NCBI:txid 221454
Compound - ID
Compound - Source
Preparation
Sample Preparation Details ID	SS01
Comment

Sample Preparation Details Information

ID	SS01
Title	Plant materials
Description	Physalis alkekengi var. franchetii and P. peruviana (Ground Cherry or Golden Berry) plants were grown in the experimental gardens of the RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan. They are not an endangered or protected species. The third fresh leaves were collected from healthy plants.
Comment_of_details

Analytical Method Information

ID	M01
Title	LC-QTOF-MS Analysis
Method Details ID	MS01
Sample Amount	1 μl
Comment

Analytical Method Details Information

ID	MS01
Title	LC-QTOF-MS Analysis
Instrument	LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	Positive
Description	The authentic samples of withanolides were isolated from plants as described in our previous paper (Ozawa et al., 2013). The leaves of P. alkekengi and P. peruviana were collected at five different developmental stages of the growing season before bearing fruit, because our pilot study showed to detect withanolides of P. alkekengi and P. peruviana at these stages (data not shown). Fresh samples of leaves at five different developmental stages were extracted with 5 μl of 80% MeOH containing 2.5 μM lidocaine (internal standard) per mg fresh weight using a mixer mill with zirconia beads (7 min at 18 Hz and 4°C). After 10-min centrifugation, the supernatant was filtered using an HLB μElution plate (Waters). The extracts (1 μl) were analyzed with LC-QTOF-MS (LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof). The analytical conditions for metabolite profiling were as described in elsewhere (Tamura et al., 2014). The polarity of electrospray ionization was applied in positive ionization mode.
Comment_of_details

PubMed (Ozawa et al., 2013)

PubMed (Tamura et al., 2014)

Data Analysis Information

ID	D01
Title	Data analysis
Data Analysis Details ID	DS01
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS01
Title	Data analysis
Description	The analytical conditions for metabolite profiling were as described in elsewhere (Tamura et al., 2014).
Comment_of_details

PubMed (Tamura et al., 2014)