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De novo genome assembly and annotation of gall-forming medicinal plant Pistacia chinensis subsp. integerrima (J. L. Stewart ex Brandis) Rech. f.

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Abstract

Pistacia chinensis subsp. integerrima is one of the medicinal plants, well known for gall formation and popularly used in Ayurveda to treat various systemic diseases such as chronic disorders, respiratory problems, etc. P. integerrima genome characterization will aid in the study of Pistacia genes and pathways involved in therapeutic application. To understand the biological characteristics of this plant and to gain the genetic insight into the biosynthesis of its natural compounds, the whole genome of P. integerrima and its leaf transcriptome was sequenced using Illumina sequencing technology. The sequenced genome was functionally annotated, and gene prediction was performed with integrated genome annotation workflow. The pathway analysis was carried out using KEGG database. We obtained a draft genome assembly of 462 Mb with N50 16,145 bp. A total of 39,452 genes were found, and 18,492 of these contained RNA or protein evidence. We characterized the genes involved in biosynthetic pathways of different plant secondary metabolites such as flavonoids and terpenoids. Also, we identified miR397 and miR828 family noncoding RNA; which mainly targets the laccase (LCA) and MYB protein functioning respectively. Phylogeneic analysis showed that P. integerrima is genetically more closer to P. vera. In this study, we attempt to explore the whole genome information of P. integerrima which will provide a genomic insight in the future for omics studies as well as serves as valuable resource for the molecular characterization of medicinal compounds.

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Acknowledgements

Authors acknowledge Dr N. B. Brindavanam for his support at every stage in this study, right from inception; Bengaluru Genomics Centre for their support in sequencing and data analysis; Dabur India Ltd. and Dr Sasibhushan Vedula for the support at various strata.

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Authors and Affiliations

  1. Center for Functional Genomics and Bioinformatics, The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India

    Santhosh N. Hegde, Noorunnisa Begum, Subrahmanya Kumar Kukkupuni, Malali Gowda & Pavithra Narendran

  2. Dabur India Limited and Dabur Research and Development Centre, 22, Site-IV, Sahiababad, Ghaziabad, 201 010, India

    Amit Bhatt, J. L. N. Sastry & S. Badrinarayan

  3. SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu, 603 203, India

    Padma Venkatasubramanian

Authors
  1. Santhosh N. Hegde
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  2. Noorunnisa Begum
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  3. Amit Bhatt
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  4. Subrahmanya Kumar Kukkupuni
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  5. Padma Venkatasubramanian
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  6. J. L. N. Sastry
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  7. S. Badrinarayan
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  8. Malali Gowda
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  9. Pavithra Narendran
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Contributions

MG designed field experiments and data generation and analysis. PN and MG were involved in sample collection. NB and AB were involved in authentic sample collection. MG and PV was involved in initiating and heading the project. SNH was involved in data analysis, interpretation and drafting manuscript. MG, PN, SK, NB and PV were involved in editing the manuscript and providing inputs.

Corresponding authors

Correspondence to Malali Gowda or Pavithra Narendran.

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Corresponding editor: Durgadas P. Kasbekar

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Hegde, S.N., Begum, N., Bhatt, A. et al. De novo genome assembly and annotation of gall-forming medicinal plant Pistacia chinensis subsp. integerrima (J. L. Stewart ex Brandis) Rech. f.. J Genet 101, 51 (2022). https://doi.org/10.1007/s12041-022-01391-w

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  • DOI: https://doi.org/10.1007/s12041-022-01391-w

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