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Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq

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Abstract

Hypericum perforatum is a traditional medicinal plant used for various purposes since ancient times because of the valuable secondary metabolites. The genomic information for H. perforatum is limited and the regulatory networks of secondary metabolism are still unknown. The naphthodianthrone hypericin is the metabolite of our main interest. It is a red-colored photodynamic pigment localized in dark glands of some Hypericum species. High-throughput sequencing technology, especially RNA-Seq, followed by de novo assembly and analysis of differential gene expression provides an important tool for functional genomics of non-model organisms. It represents an opportunity of insight into dynamic biological processes including those of secondary metabolism. Transcriptome analysis followed by the analysis of differential gene expression of H. perforatum leaf tissues containing and lacking dark glands was performed to identify the genes involved in hypericin biosynthesis and to profile expression patterns in greater detail. A total of 18.53 G of cleaned read nucleotides were generated and assembled into 139,959 contigs with N50 of 1801 bp. Among them, 66,817 (47.74 %) contigs were annotated. Differentially expressed genes were discovered by comparison of dark glands with adjacent leaf tissue and contrasting inner part leaf tissue without dark glands. A total of 799 upregulated genes were found in the tissues containing dark glands and 263 enzymes were identified, including candidate genes of hypericin biosynthesis, especially the genes coding for polyketide synthases and those involved in defense reactions. This study determined candidate genes involved in hypericin biosynthesis providing a valuable source for perspective metabolic engineering of bioactive substances.

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Acknowledgments

This research was supported by the Slovak Research and Development Agency APVV-14-0154, the Scientific Grant Agency of Slovak Republic VEGA 1/0090/15, and the grant project SOFOS-knowledge and skill development of staff, students of P. J. Šafárik University in Košice (contract number: 003/2013/1.2/OPV, ITMS code: 26110230088), funded by the European Social Fund through the Operational Program Education and KVARK (ITMS code: 26110230084). We thank Peter Pisarčík, Maroš Andrejko, Tomáš Horváth, and Gabriel Semanišin from Institute of Computer Sciences, Faculty of Science, Pavol Jozef Šafárik University, in Košice and Libuse Brachova from Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, for support.

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Authors and Affiliations

  1. Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, 041 54, Košice, Slovakia

    Miroslav Soták, Odeta Czeranková, Katarína Nigutová & Eva Čellárová

  2. Institute of Mathematics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Jesenná 5, 040 01, Košice, Slovakia

    Daniel Klein

  3. Department of Molecular Genetics, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Stadt Seeland, Germany

    Lothar Altschmied

  4. Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011-3260, USA

    Ling Li & Eve Syrkin Wurtele

  5. Center for Metabolic Biology, Iowa State University, Ames, IA, 50011-3260, USA

    Ling Li & Eve Syrkin Wurtele

  6. Bioinformatics and Computational Biology, NFS Engineering Research Center for Bio Renewable Chemicals, Iowa State University, Ames, IA, 50011-3260, USA

    Adarsch Jose

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  1. Miroslav Soták
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Corresponding author

Correspondence to Miroslav Soták.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1: Table S1

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as oxidoreductases. (DOCX 32 kb)

ESM 2: Table S2

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as transferases. (DOCX 38 kb)

ESM 3: Table S3

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as hydrolases. (DOCX 37 kb)

ESM 4: Table S4

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as lyases. (DOCX 15 kb)

ESM 5: Table S5

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as isomerases. (DOCX 12 kb)

ESM 6: Table S6

Upregulated differential expressed genes of dark glands with adjacent leaf tissue of H. perforatum annotated as ligases. (DOCX 14 kb)

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Soták, M., Czeranková, O., Klein, D. et al. Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq. Plant Mol Biol Rep 34, 1027–1041 (2016). https://doi.org/10.1007/s11105-016-0982-2

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  • DOI: https://doi.org/10.1007/s11105-016-0982-2

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