PJB-2019-551
The relationship of synonymous codon usage bias analyses of stress resistant and reference genes in significant species of plants
Syed Qasim Shah, Nayab Khan, Syed Umair Ahmad, Zohaib Bashir and Tariq Mahmood
Abstract
The Synonymous Codon Usage Bias (SCUB) corresponds to the difference in the expression level of a gene that interrupts the quantity of proteins and varies the expression level of a protein. Stress associated with dehydration, cold, heat, salt, heavy metals, oxidative and drought also lessen the yield of significant plants. This research is centered upon the CUB and RNA structures (RS) analyses of abiotic stress resistant and reference genetic material in significant species of dicot (Arabidopsis thaliana, Populous trichocarpa) and monocot (Oryza sativa and Triticum aestivum) plants. Precisely, 11 stress resistant and 3 reference genes were subjected to SCUB and RS analysis. SCUB analysis revealed that O. sativa presented 82%, P. trichocarpa 91% and T. aestivum with about 55% similarity with A. thaliana in the utilization of synonymous codons for abiotic stress resistant genes. The Reference genes for O. sativa and P. trichocarpa each manifest 100% similarities with A. thaliana except for the T. aestivum that exhibit 67% similarities in the usage of codons. Mfold algorithms were implemented for the prediction of RNA Secondary Structures (RSS) of abiotic stress resistant and Reference genes, the Dicot species expressed a significant difference in the MFE with the Monocot species; however, there were no significant difference in the number of stems and loops. The Reference genes indicated a random behavior for MFE, number of stems and loops. Most preferred codons were calculated for stress resistant and Reference genes via gene infinity software. SCUB and RSS results will be supportive to encounter numerous stress resistant crops across codon optimization
To Cite this article:
Shah, S.Q., N. Khan, S.U. Ahmad, Z. Bashir and T. Mahmood. 2021. The relationship of synonymous codon usage bias analyses of stress resistant and reference genes in significant species of plants. Pak. J. Bot., 53(3): DOI: http://dx.doi.org/10.30848/PJB2021-3(32)
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