scholarly journals The relationship between codon usage bias and salt resistant genes in Arabidopsis thaliana and Oryza sativa

2012 ◽  
Vol 1 (2) ◽  
pp. 48-51 ◽  
Author(s):  
Muhammad Younas Khan Barozai
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Resistant Genes ◽  
The Relationship

Synonymous codon usage bias in Oryza sativa

Plant Science ◽  
2004 ◽  
Vol 167 (1) ◽  
pp. 101-105 ◽  
Author(s):  
Qingpo Liu ◽  
Ying Feng ◽  
Xin’ai Zhao ◽  
Hui Dong ◽  
Qingzhong Xue
Keyword(s):  
Oryza Sativa ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Synonymous Codon Usage Bias

scholarly journals Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Li Gun ◽  
Ren Yumiao ◽  
Pan Haixian ◽  
Zhang Liang
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Strong Negative Correlation ◽  
Synonymous Codons ◽  
The Relationship ◽  
Adaptation Index

Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G3, GC12, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A3/(A3+T3) and G3/(G3+C3), GC12 versus GC3 plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC3 and GC12) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.

scholarly journals Patterns of Codon Usage Bias in WRKY Genes of Brassica rapa and Arabidopsis thaliana

2019 ◽  
Vol 11 (4) ◽  
pp. 76
Author(s):  
Snigdha Srivastava ◽  
Sheetal Chanyal ◽  
Ashutosh Dubey ◽  
A. K. Tewari ◽  
Gohar Taj
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Codon Usage ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Codon Usage Bias ◽  
Wrky Transcription Factor ◽  
Codon Usage Pattern ◽  
Transcription Factor Family ◽  
Synonymous Codons

Codon usage bias (CUB) is defined as the selective and nonrandom use of synonymous codons by the organism for encoding the amino acids. One of the important plant transcription factor family is the ‘WRKY’ whose role has been investigated in the regulation of abiotic and biotic stress responses in plants. In this paper, the codon usage pattern of the WRKY transcription factor of the two important plant species Arabidopsis thaliana and Brassica rapa has been investigated. Various codon usage indices like ENc, CAI, correspondence analysis, RSCU analysis, neutrality plot and hierarchial clustering has been done. The GC codon status was high in Arabidopsis. The RSCU analysis of codons revealed that codons coding for arginine was maximum in both the plant species.Our results propose that natural selection was the main dominating factor guiding the evolution of different WRKY genes in both Arabidopsis thaliana and Brassica rapa.

scholarly journals Stress induced MAPK genes show distinct pattern of codon usage in Arabidopsis thaliana, Glycine max and Oryza sativa

2014 ◽  
Vol 10 (7) ◽  
pp. 436-442 ◽  
Author(s):  
H Surachandra Singha ◽  
◽  
Supriyo Chakraborty ◽  
Himangshu Deka ◽  
◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Oryza Sativa ◽  
Glycine Max ◽  
Codon Usage ◽  
Distinct Pattern
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