Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms

2018 ◽  
Vol 219 ◽  
pp. 24-32 ◽  
Author(s):  
Bornali Deb ◽  
Arif Uddin ◽  
Gulshana Akthar Mazumder ◽  
Supriyo Chakraborty
Keyword(s):  
Codon Usage ◽  
Mitochondrial Protein ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals In silico prediction of mtDNA Gene Expression Based on Codon Usage Bias in Ants (Formicidae Latreille, 1802) that Inhabit Limestone Quarry Ecosystems

2018 ◽  
Vol 2 (1) ◽  
pp. 32
Author(s):  
Semir Dorić ◽  
Dinko Osmanković ◽  
Lada Lukić Bilela
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
In Silico ◽  
Expression Patterns ◽  
Mitochondrial Protein ◽  
Model Organisms ◽  
Molecular Response ◽  
Protein Coding ◽  
Protein Coding Genes

Codon usage is considered as a modulator of gene expression, due to high correlation between codon usage, tRNA abundance and the level of gene expression. Adaptability is primarily manifested at gene level therefore mtDNA gene expression analysis may indicate trends toward the development of adaptive traits for specific environmental conditions. Moreover, modified gene expression patterns may result from such adaptations. Due to their sensitivity to environmental disturbances, great functional importance and accessibility ants (Family: Formicidae Latreille, 1802) are excellent model organisms for  molecular and bioinformatics genome analysis. This in silico simulation is based on the comparison of codon usage bias and the level of gene expression of currently available mitochondrial protein-coding genes of ant species that were sampled at quarry Ribnica (Kakanj, Bosnia and Herzegovina). MILC and MELP algorithms were used forcodon usage bias analysis and mitochondrial gene expression prediction, respectively. The analysis included four mtDNA protein-coding genes from eight selected species of ants totaling in 32 protein sequences. The results of codon usage analysis indicated no statistically significant differences in codon usage bias, as well as relative frequencies of the gene expression level.  The next step should be directed to molecular ecology studies, even using whole genome measures of gene expression (RNA-seq; transcriptomics) to capture molecular response to environmental challenges.

Polyphyletic Origins of Schizothoracinae Fishes (Cyprinidae) in Respect to Their Mitochondrial Protein-Coding Genes

2019 ◽  
Vol 07 (02) ◽  
Author(s):  
Saira Bibi ◽  
Muhammad Fiaz Khan ◽  
Aqsa Rehman ◽  
Faisal Nouroz
Keyword(s):  
Mitochondrial Protein ◽  
Protein Coding ◽  
Protein Coding Genes

Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 537-548 ◽  
Author(s):  
Sudhir Kumar
Keyword(s):  
Nucleotide Substitution ◽  
Mitochondrial Protein ◽  
Likelihood Estimation ◽  
Nucleotide Composition ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Conserved Genes ◽  
Maximum Likelihood Methods ◽  
Position Data

Abstract Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the lst+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition / transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for lst+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.

scholarly journals Analysis of codon usage bias of classical swine fever virus

2021 ◽  
pp. 1450-1458
Author(s):  
Sharanagouda S. Patil ◽  
Uma Bharathi Indrabalan ◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Bibek Ranjan Shome
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Principal Component ◽  
Infectious Agent ◽  
Classical Swine Fever ◽  
Economic Loss ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Coding Regions

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

The codon usage pattern of genes involved in ovarian cancer

2019 ◽  
Vol 1440 (1) ◽  
pp. 67-78 ◽  
Author(s):  
Arif Uddin ◽  
Nirmal Paul ◽  
Supriyo Chakraborty
Keyword(s):  
Ovarian Cancer ◽  
Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern
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