scholarly journals Codon usage bias analysis for the coding sequences of Camellia sinensis and Brassica campestris

2016 ◽  
Vol 15 (8) ◽  
pp. 236-251 ◽  
Author(s):  
Paul Prosenjit ◽  
Chakraborty Supriyo
Keyword(s):  
Codon Usage ◽  
Camellia Sinensis ◽  
Codon Usage Bias ◽  
Brassica Campestris ◽  
Bias Analysis ◽  
Coding Sequences

scholarly journals Codon usage bias analysis for the spermidine synthase gene from Camellia sinensis (L.) O. Kuntze

2015 ◽  
Vol 14 (3) ◽  
pp. 7368-7376 ◽  
Author(s):  
E. You ◽  
Y. Wang ◽  
Z.T. Ding ◽  
X.F. Zhang ◽  
L.L. Pan ◽  
...  
Keyword(s):  
Codon Usage ◽  
Camellia Sinensis ◽  
Codon Usage Bias ◽  
Spermidine Synthase ◽  
Bias Analysis

scholarly journals Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1087 ◽  
Author(s):  
Sheng-Lin Shi ◽  
Run-Xi Xia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Effective Number ◽  
Bias Analysis ◽  
The Family ◽  
Usage Patterns ◽  
Codon Positions ◽  
Effective Number Of Codons

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

scholarly journals CodonO: codon usage bias analysis within and across genomes

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W132-W136 ◽  
Author(s):  
M. C. Angellotti ◽  
S. B. Bhuiyan ◽  
G. Chen ◽  
X.-F. Wan
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Bias Analysis

scholarly journals Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 331 ◽  
Author(s):  
Kajal Biswas ◽  
Supratik Palchoudhury ◽  
Prosenjit Chakraborty ◽  
Utpal Bhattacharyya ◽  
Dilip Ghosh ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Citrus Tristeza Virus ◽  
Synonymous Codon ◽  
Management Strategies ◽  
Bias Analysis ◽  
Mutation Pressure ◽  
Usage Patterns ◽  
Tristeza Virus ◽  
Citrus Tristeza

Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.

scholarly journals Codon usage bias in 5′ terminal coding sequences reveals distinct enrichment of gene functions

Genomics ◽  
2017 ◽  
Vol 109 (5-6) ◽  
pp. 506-513 ◽  
Author(s):  
Huiling Liu ◽  
Siddiq Ur Rahman ◽  
Yuanhui Mao ◽  
Xiaodong Xu ◽  
Shiheng Tao
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Coding Sequences ◽  
Gene Functions

scholarly journals Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaoting Yao ◽  
Qinlei Fan ◽  
Bo Yao ◽  
Ping Lu ◽  
Siddiq Ur Rahman ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Bluetongue Virus ◽  
Bias Analysis

scholarly journals Codon Usage Bias Prefers AT Bases in Coding Sequences Among the Essential Genes of Haemophilus influenzae

2014 ◽  
Vol 6 (4) ◽  
pp. 417-421 ◽  
Author(s):  
Chakraborty SUPRIYO ◽  
Paul PROSENJIT ◽  
Tarikul Huda MAZUMDER
Keyword(s):  
Gene Expression ◽  
Haemophilus Influenzae ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Compositional Analysis ◽  
Revealed Preference ◽  
Nucleotide Composition ◽  
Essential Genes ◽  
Coding Sequences ◽  
Codon Positions

The base composition at three different codon positions in relation to codon usagebias and gene expressivity was studied in a sample of twenty five essential genes from Haemophilus influenzae. ENC, CBI and Fop were used to quantify the variation in codon usage bias for the cds. CAI is used to estimate the level of gene expression of the cds selected in the present study. To find out the relationship between the extent of codon bias and nucleotide composition the values of A, T, G, C and GC they were compared with the A3, T3, G3, C3 and GC3 values, respectively. The results showed relatively weak codon usage bias among the coding sequences (cds) of Haemophilus influenzae. This in turn, implies that the essential genes prefer to use a set of restricted codons. However, the base compositional analysis of essential genes in Haemophilus influenzae revealed preference of AT to GC bases within their coding sequences and this preference might affect gene expression as indicated by the relatively high CAI values ofthe coding sequences.

scholarly journals Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 81
Author(s):  
Hua Feng ◽  
Joaquim Segalés ◽  
Fangyu Wang ◽  
Qianyue Jin ◽  
Aiping Wang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Large Scale ◽  
Codon Usage Pattern ◽  
Major Protein ◽  
Mutation Pressure ◽  
Coding Sequences ◽  
Usage Patterns ◽  
Porcine Circoviruses

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

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