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In Silico Identification of miRNA and Targets from Chrysopogon zizanioides (L.) Roberty with Functional Validation from Leaf and Root Tissues

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Abstract

microRNAs are small non-coding RNA molecule that plays an important role in metabolism. Chrysopogon zizanioides (L.) Roberty is an important aromatic plant used in perfumery industries, soil, water conservation, and agricultural practices. In this study, the transcriptomic sequence of vetiver leaf and root was subjected to miRNA identification by the computational methods. miRNA identification was carried out using a homology-based method by C-mii software with several other online tools. A total of 80 miRNA were identified from both leaf and root sequences. Target identification was done by identified miRNA sets. A total of 25 and 31 miRNA families were identified in both leaf and root, respectively, with ten common families involve in different ontological function. miR169 and miR5021 regulate most of the target in leaf and root. In vetiver, many primary and secondary metabolism elements are regulated by miRNA as photo-system, transcription factor, terpenoid metabolism, etc. Here is the first in silico study revealing the specific miRNAs and their target genes for corresponding root and leaf tissues respectively in C. zizanioides.

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Funding

The authors are thankful for the support and facilities provided by the Director, CSIR-CIMAP, UP, Lucknow, India. This research work is supported by the Council of Scientific and Industrial Research, India, under CSR-Emeritus Scientist Scheme funding via Sanction No. 21 (1020)/16/EMR-II dated 18-11-2016. Anand Mishra acknowledges the CSIR-Research associate fellowship and the funds granted from CSIR, New Delhi, India.

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Authors and Affiliations

  1. Genetics and Plant Breeding Division, CSIR-Central Institute for Medicinal and Aromatic Plants, Lucknow, UP, 226015, India

    Anand Mishra & Raj Kishori Lal

  2. Bioinformatics Department, CSIR-National Botanical Research Institute, Lucknow, UP, 226001, India

    Sanchita Gupta

  3. Biotechnology Division, CSIR-Central Institute for Medicinal and Aromatic Plants, U P, Lucknow, 226015, India

    Pankhuri Gupta & Sunita Singh Dhawan

  4. CSIR-Human Resource Development Centre Campus, Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India

    Pankhuri Gupta

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AM was involved in planning, actual experimentation, and statistical analyses; S helped in in silico analysis; PG helped in data collection; SSD helped in data analysis; and RKL was involved in manuscript preparation

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Mishra, A., Gupta, S., Gupta, P. et al. In Silico Identification of miRNA and Targets from Chrysopogon zizanioides (L.) Roberty with Functional Validation from Leaf and Root Tissues. Appl Biochem Biotechnol 192, 1076–1092 (2020). https://doi.org/10.1007/s12010-020-03381-z

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