Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Fukushima A

PROVIDER: S-EPMC5167740 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

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

Fukushima Atsushi A Nakamura Michimi M Suzuki Hideyuki H Yamazaki Mami M Knoch Eva E Mori Tetsuya T Umemoto Naoyuki N Morita Masaki M Hirai Go G Sodeoka Mikiko M Saito Kazuki K

Frontiers in plant science 20161220

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 pote ...[more]

PMID: 28066454

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Project description:BACKGROUND:Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. RESULTS:We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371?bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638?bp and 354?bp, respectively. Functional annotation was performed using NCBI's BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. CONCLUSIONS:We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S. lycopersicum, S. tuberosum, Capsicum spp, S. melongena and Petunia spp.

Dataset Information

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

Publications

Comparative Characterization of the Leaf Tissue of <i>Physalis alkekengi</i> and <i>Physalis peruviana</i> Using RNA-seq and Metabolite Profiling.

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