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De novo transcriptome analysis unravels tissue-specific expression of candidate genes involved in major secondary metabolite biosynthetic pathways of Plumbago zeylanica: implication for pharmacological potential

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Abstract

Key message

The present study provides comparative transcriptome analysis, besides identifying functional secondary metabolite genes of Plumbago zeylanica with pharmacological potential for future functional genomics, and metabolomic engineering of secondary metabolites from this plant towards diversified biomedical applications.

Abstract

Plumbago zeylanica is a widely used medicinal plant of the traditional Indian system of medicine with wide pharmacological potential to treat several disorders. The present study aimed to carry out comparative transcriptome analysis in leaf and root tissue of P. zeylanica using Illumina paired end sequencing to identify tissue-specific functional genes involved in the biosynthesis of secondary metabolites, contributing to its therapeutic efficacy. De novo sequencing assembly resulted in the identification of 62,321 “Unigenes” transcripts with an average size of 1325 bp. Functional annotation using BLAST2GO resulted in the identification of 50,301 annotated transcripts (80.71%) and GO assigned to 18,814 transcripts. KEGG pathway annotation of the “Unigenes” revealed that 2465 transcripts could be assigned to 242 KEGG pathway maps wherein the number of transcripts involved in secondary metabolism was distinct in root and leaf transcriptome. Among the secondary metabolite biosynthesis pathways, the cluster of “Unigenes” encoding enzymes of ‘Phenylpropanoid biosynthesis pathway’ represents the largest group (84 transcripts) followed by ‘Terpenoid Backbone biosynthesis’ (48 transcripts). The transcript levels of the candidate unigenes encoding key enzymes of phenylpropanoid (PAL, TAL) and flavanoid biosynthesis (CHS, ANS, FLS) pathways were up-regulated in root, while the expression levels of candidate “Unigenes” transcript for monoterpenoid (DXS, ISPF), diterpenoid biosynthesis (SPS, SDS) and indole alkaloid pathways (STR) were significantly higher in leaf of P. zeylanica. Interestingly, validation of differential gene expression profile by qRT-PCR also confirmed that candidate “Unigenes” enzymes of phenylpropanoid and flavonoid biosynthesis were highly expressed in the root, while the key regulatory enzymes of terpenoid and indole alkaloid compounds were up-regulated in the leaf, suggesting that (differences in) the levels of these functional genes could be attributed to the (differential) pharmacological activity (between root and leaf) in tissues of P. zeylanica.

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Acknowledgements

The author Karpaga Raja Sundari acknowledges DST-National Post-Doctoral Fellowship for funding this research work. KRS also acknowledges the support of Dr. Modhumita Dasgupta, Scientist F, Institute of Forest Genetics and Tree Breeding, Coimbatore, for providing the guidance and facilities to carry out RNA extraction from tissues of P. zeylanica. The study was funded by Science and Engineering Research Board(SERB) (Grant no. DST/NPDF/2015/000524).

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  1. Central Research Facility, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, India

    Balachandran Karpaga Raja Sundari, Bilikere S. Dwarakanath & S. P. Thyagarajan

  2. Bionivid Technology [P] Limited, Kasturi Nagar, Bangalore, 560043, India

    Roli Budhwar

  3. Shanghai Proton and Heavy Ion Center, Pudong, 201321, Shanghai, China

    Bilikere S. Dwarakanath

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  1. Balachandran Karpaga Raja Sundari
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Contributions

The author BKRS and SPT conceptualized and designed the experiments for RNA sequencing. RB contributed to RNA sequencing and acquisition of data while BKRS and RB analyzed the transcriptome data. BKRS conducted experimental validation by qRT-PCR for the obtained transcripts. BKRS and BSD interpreted the data and drafted the article. BSD and SPT critically revised the article and made the final approval of the manuscript.

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Correspondence to Balachandran Karpaga Raja Sundari.

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Conflict of interest

The corresponding author, Karpaga Raja Sundari has received grant from Department of science and Technology, Govt. of India. All the authors declare that they have no competing financial and non-financial interests.

Data archiving statement

P. zeylanica leaf and root transcriptome raw data can be accessed at NCBI SRA database under SRA ID SRP144988.

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Karpaga Raja Sundari, B., Budhwar, R., Dwarakanath, B.S. et al. De novo transcriptome analysis unravels tissue-specific expression of candidate genes involved in major secondary metabolite biosynthetic pathways of Plumbago zeylanica: implication for pharmacological potential. 3 Biotech 10, 271 (2020). https://doi.org/10.1007/s13205-020-02263-9

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