Author(s): Himanshu Singh, Nooman Siddique, Atul Kumar Upadhyay


DOI: 10.5958/0974-360X.2020.00314.5   

Address: Himanshu Singh1, Nooman Siddique1, Atul Kumar Upadhyay2
1School of Bioengineering and Biosciences, Lovely Professional University, Punjab.
2Department of Biotechnology, Thapar University, Punjab.
*Corresponding Author

Published In:   Volume - 13,      Issue - 4,     Year - 2020

Plants are able to produce numerous types of metabolites, which can be utilized for drug development, and various other purposes like resistance to a pest, abiotic stresses, and disease. Recently it was discovered that genes, which are responsible for the production of these metabolites, are arranged in operon-like gene clusters. These gene clusters are co-expressed and regulated by the same set of regulatory elements. Identification of such gene clusters has tremendous application in synthetic biology. Advancement in genome information, genome mining, and analysis tools have placed us at a commanding position that will provide us a technique to modify the gene for large production of the specialized chemicals. Rice being stapled food for the majority of the human population is chosen in the present study to find out the gene clusters responsible for the production of secondary metabolites. We have reported 39 gene clusters on 12 chromosomes of Oryza sativa group Japonica. Few of the selected metabolite producing gene clusters is a saccharide, lignin, terpene, alkaloid etc. There were several gene clusters for putative metabolites, which we have annotated in this study.

Cite this article:
Himanshu Singh, Nooman Siddique, Atul Kumar Upadhyay. Genome-wide Identification and Annotation of metabolite producing Gene Clusters in Rice Genome. Research J. Pharm. and Tech. 2020; 13(4):1744-1746. doi: 10.5958/0974-360X.2020.00314.5

Himanshu Singh, Nooman Siddique, Atul Kumar Upadhyay. Genome-wide Identification and Annotation of metabolite producing Gene Clusters in Rice Genome. Research J. Pharm. and Tech. 2020; 13(4):1744-1746. doi: 10.5958/0974-360X.2020.00314.5   Available on:

1.    Yi, G., Sze, S.-H., and Thon, M. R. (2007). Identifying clusters of functionally related genes in genomes. Bioinformatics (Oxford, England), 23(9), 1053–1060. bioinformatics/btl673
2.    Osbourn, A. (2010). Secondary metabolic gene clusters: Evolutionary toolkits for chemical innovation. Trends in Genetics, 26, 449–457
3.    D’Auria, J. C., and Gershenzon, J. (2005). The secondary metabolism of Arabidopsis thaliana: Growing like a weed. Current Opinion in Plant Biology, 8, 308–316.
4.    Ghosh, B., Ali, M.N. and Gantait, S. (2016). Response of Rice under Salinity Stress: A Review Update. J. Res. Rice, 4(2): 2–9.
5.    Osbourn, A., and Field, B. (2009). Operons. Cellular and Molecular Life Sciences, 66, 37555–37575.
6.    Wang, S., Takahashi, H., Kajiura, H., Kawakatsu, T., Fujiyama, K., and Takaiwa, F. (2013). Transgenic rice seeds accumulating recombinant hypoallergenic birch pollen allergen Bet v 1 generate giant protein bodies. Plant and Cell Physiology, 54(6), 917–933.
7.    Kemmerer, E. C., Lei, M., and Wu, R. (1991). Isolation and molecular evolutionary analysis of a cytochrome c gene from Oryza sativa (rice). Molecular Biology and Evolution, 8(2), 212–226.
8. Qin, F.-J., Sun, Q.-W., Huang, L.-M., Chen, X.-S., and Zhou, D.-X. (2010). Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression. Molecular Plant, 3(4), 773– 782. 10.1093/mp/ssq030
9.    Samanani, N., Liscombe, D. K., and Facchini, P. J. (2004). Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis. The Plant Journal : For Cell and Molecular Biology, 40(2), 302—313.
10.    Stöckigt, J., Barleben, L., Panjikar, S., and Loris, E. A. (2008). 3D-Structure and function of strictosidine synthase-- the key enzyme of monoterpenoid indole alkaloid biosynthesis. Plant Physiology and Biochemistry : PPB, 46(3), 340—355. 10.1016/j.plaphy.2007.12.011
11.    Wen, J., Vanek-Krebitz, M., Hoffmann-Sommergruber, K., Scheiner, O., and Breiteneder, H. (1997). The potential of Betv1 homologues, a nuclear multigene family, as phylogenetic markers in flowering plants. Molecular Phylogenetics and Evolution, 8(3), 317—333.
12.    Ritika Chauhan, Nidhi Singh, Jayanthi Abraham. Bioactivity and Molecular Docking of Secondary Metabolites produced by Streptomyces xanthochromogenes JAR5. Research J. Pharm. and Tech. 8(3): Mar., 2015; Page 300-309.
13.    Prabhjot Kour, Anupam Tiwari. Medicinal Values of Secondary Metabolites of Withania Somnifera. Research J. Pharm. and Tech 2018; 11(7): 3167-3170.
14.    Savita More, Vijay Raje, Namita Phalke, Sarika Lokhande. Bioinformatics – An Emerging Field. Asian J. Res. Pharm. Sci. 2018; 8(4): 185-191.
15.    Neeraj Upmanyu, Surya Gupta, B N Prakash, Gopal Garg, P Mishra. Cheminformatics: A New Approach. Research J. Pharm. and Tech. 1(1): Jan.-Mar. 2008; Page 2-5.

Recomonded Articles:

Research Journal of Pharmacy and Technology (RJPT) is an international, peer-reviewed, multidisciplinary journal.... Read more >>>

RNI: CHHENG00387/33/1/2008-TC                     
DOI: 10.5958/0974-360X 

56th percentile
Powered by  Scopus

SCImago Journal & Country Rank

Recent Articles


Not Available