In Silico Identification of miRNA and Targets from Chrysopogon zizanioides (L.) Roberty with Functional Validation from
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In Silico Identification of miRNA and Targets from Chrysopogon zizanioides (L.) Roberty with Functional Validation from Leaf and Root Tissues Anand Mishra 1 Raj Kishori Lal 1
2
& Sanchita Gupta & Pankhuri Gupta
3,4
3
& Sunita Singh Dhawan &
Received: 19 February 2020 / Accepted: 23 June 2020/ # Springer Science+Business Media, LLC, part of Springer Nature 2020
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 photosystem, 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. Keywords C. zizanioides . Essential oil . miRNA . Network . Target identification
Introduction Chrysopogon zizanioides (L.) Roberty (syn. Vetiveria zizanioides (L.) Nash) is a C4 perennial herbaceous grass of the family Poaceae which is popularly known as “khus” and vetiver grass and is a basic ingredient for modern medicines, cosmetic, and perfumery industries [1]. Despite India and
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12010-02003381-z) contains supplementary material, which is available to authorized users.
* Anand Mishra [email protected] Extended author information available on the last page of the article
Applied Biochemistry and Biotechnology
Africa origin, it is found in the wild, tropical, and Mediterranean climates in every part of the world [2].Vetiver root contains the high-valued essential oil [3]. In the global market, Indonesia, Haiti, and India are the leading producers of vetiver oil. In India, vetiver is mainly cultivated in Uttar Pradesh, Rajasthan, Bihar, and various regions of the southern and peninsular part [4]. The global market scenario for vetiver oil production is approximated to be 600–700 tons per year, while India produced only 20–25 tons annually [2]. All parts of the plant are useful in the medicinal system and generally used as ointment and treatment in disease [3]. Vetiver plant possesses the specific morphological feature such as having a strong, deep penetrating, aerenchymatous, and fast-growing root system. A
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