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. 2022 Jun 30:13:930113.
doi: 10.3389/fgene.2022.930113. eCollection 2022.

In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses

Vrantika Chaudhary  1 , Sumit Jangra  1 , Neelam R Yadav  1
Affiliations

In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses

Vrantika Chaudhary et al. Front Genet. .

Abstract

Cluster bean popularly known as "guar" is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8-177.3 (-kcal/mol) with an average value of 25.4 (-kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.

Keywords: cluster bean (Cyamopsis tetragonoloba L. Taub.); galactomannan; miRNA identification; miRNA targets; micro RNAs (miRNAs); non coding RNAs.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Workflow for identification of miRNA and their targets in cluster bean.
FIGURE 2
FIGURE 2
Identified miRNA families of cluster bean which have homologues in other plant species (ath- Arabidopsis thaliana, osa-Oryza sativa, gma-Glycine max, mtr-Medicago truncatula, zma-Zea mays, vvi-Vitis vinifera, sof-Saccharum officinarum, pab-Picea abies, aly-Arabidopsis lyrata, smo-Selaginella moellendorffii, tae-Triticum aesativum, cre-Chlamydomonas reinhardtii, pta- Pinus taeda, ppt-Physcomitrella patens).
FIGURE 3
FIGURE 3
Phylogenetic relationship among predicted miRNA families in cluster bean.
FIGURE 4
FIGURE 4
GO annotation for output targets and their distribution in three categories (A) Molecular function (B) Biological process (C) Cellular component.
FIGURE 5
FIGURE 5
Gene regulatory networks of cluster bean target genes in GENEMANIA against Arabidopsis thaliana.
FIGURE 6
FIGURE 6
Major transcription factor classes identified from cluster bean ESTs.
FIGURE 7
FIGURE 7
A proposed model of interactions among transcription factors and miRNAs for gene regulation in cluster bean.
See this image and copyright information in PMC

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References

    1. Acharya B. R., Sandhu D., Dueñas C., Ferreira J. F. S., Grover K. K. (2022). Deciphering Molecular Mechanisms Involved in Salinity Tolerance in Guar (Cyamopsis tetragonoloba (L.) Taub.) Using Transcriptome Analyses. Plants 11 (3), 291. 10.3390/plants11030291 - DOI - PMC - PubMed
    1. Al-Qurainy F., Alshameri A., Gaafar A. R., Khan S., Nadeem M., Alameri A. A., et al. (2019). Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. Int. J. Genomics. 2019, 7295859. 10.3390/plants1103029110.1155/2019/7295859 - DOI - PMC - PubMed
    1. Bansal A., Singh T. R., Chauhan R. S. (2017). A Novel miRNA Analysis Framework to Analyze Differential Biological Networks. Sci. Rep. 7 (1), 14604. 10.1038/s41598-017-14973-x - DOI - PMC - PubMed
    1. Bartel D. P. (2004). MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116 (2), 281–297. 10.1016/S0092-8674(04)00045-5 - DOI - PubMed
    1. Bhatt R. K., Sharma R., Mahla H. R., Kalia R. K. (2016). Guar Production, Utilization and Marketing: Current Scenario and Future Prospects. Jodhpur: Central Arid Zone Research Institute, 1–40.