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Scatter plot of CAI with Axis 1 CAI and codon usage variation: role of gene expressivity Codon Adaptation Index (CAI) has been extensively used as a measure of gene expression level in organisms. Within T. elongatus genome, CAI showed positive correlation with the positions of genes along axis 1 and GC3s ( r = 0.274 and r= 0.229 respectively, P<0.01) (Figure 4) but was negatively correlated with Nc (r =0.389). This has reflected the effect of gene expression level on codon selection pattern in T. elongatus. Data suggested that genes with higher expression level exhibing a greater degree of codon usage bias were distributed at right side of the first axis and prefered to use G-or C-ending codons. This result indicated a role of expression levels of genes in codon usage variation along with compositional constraints and supported the argument of presence of additional factors along with compositional constraint in shaping the codon usage bias in this genome. Furthermore, CAI showed a positive correlation with C3s (r = 0.605, P <0.01) whereas negative correlation with G3s (r =-0.243, P <0.01) supporting our hypothesis that the influence of mutational bias is reflected in the choice of bases in the third codon position and thus, favor translational selection.
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Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in...
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... for translational accuracy is predicted to have a positive correlation between codon bias and gene length [15]. From the plot drawn with gene length against Nc (Figure 2), it is clear that shorter genes have a much wider variance in Nc values and vice versa for longer genes. Lower Nc values of longer genes may be expected due to the direct effect of translation time on fitness or to the extra energy cost associated with longer translational timing. Correlation analyses between gene length and gene position on axis 1, GC3s and Nc values (r = 0.158, 0.170 and -0.173, respectively, P< 0.01) were all significantly correlated. The observed significant correlation in T. elongatus genome revealed that gene length influences codon usage of this organism. Gene length was negatively correlated with Nc (r = -0.173) but it showed positive correlation with GC3s (r = 0.170). Therefore, codon bias is lower in longer genes than in shorter ones (Figure 3). It is meaningful that up to certain extent, translational accuracy also plays a role in dictating the codon usage variation in this genome. (Figure 4) but was negatively correlated with Nc (r =0.389). This has reflected the effect of gene expression level on codon selection pattern in T. elongatus. Data suggested that genes with higher expression level exhibing a greater degree of codon usage bias were distributed at right side of the first axis and prefered to use G-or C-ending codons. This result indicated a role of expression levels of genes in codon usage variation along with compositional constraints and supported the argument of presence of additional factors along with compositional constraint in shaping the codon usage bias in this genome. Furthermore, CAI showed a positive correlation with C3s (r = 0.605, P <0.01) whereas negative correlation with G3s (r = -0.243, P <0.01) supporting our hypothesis that the influence of mutational bias is reflected in the choice of bases in the third codon position and thus, favor translational ...
Citations
... In most of the species a significant negative correlation between Nc and GC3 was depicted, a trend well in line with the standard notion of Nc-GC3 relationship (Hassan et al., 2009;Pandit and Sinha, 2011;Prabha et al., 2012;Malakar et al., 2016Malakar et al., , 2019Song et al., 2017b). The results of the correlation analysis is shown in Supplementary Table 3. ...
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
... One of the objectives of this study is to investigate the codon usage in the genomes of different cyanobacterial species that belong to diverse habitats and present different physiological and morphological characteristics. Although some studies have been conducted on the codon usage in certain closely related cyanobacterial genomes (Campbell and Gowri, 1990;Prabha et al., 2012;Yu et al., 2012;Xu et al., 2013), a comprehensive genome-wide analysis representing major taxonomic groups of cyanobacteria is lacking. We analyzed codon usage bias and codon context patterns among 41 sequenced cyanobacterial genomes representing five different taxonomic orders. ...
... All the 16 cyanobacterial genomes with Nc higher than 50 were associated with GC3s ranging between 0.3 and 0.6 (Fig. 2). Nc plot indicated that factors other than the compositional bias are also influencing codon usage bias of the genes as suggested by Hassan et al. (2009) and Prabha et al. (2012). It also revealed that many cyanobacteria, majority of which are members of Prochlorales lied very close to expected curve supporting that compositional constraint is major factor in shaping codon usage bias of these organisms. ...
... Study of codon usage is valuable due to its importance in the perception of the molecular basics plus potential utilization as a molecular marker for typifying molecular evolution. Oligonucleotide probes and DNA primers can also be designed for catching genes of interest based on this knowledge as well (Prabha et al., 2012). Likely selection patterns due to varying environmental factors effect gene expressivity and codon usage trend among genes in different species of bacteria (McInerney, 1997). ...
Barbiturases exist solely in bacteria and encompass an undistinguished protein family. s-Triazine compound introduction into the environment owing to recent industrial practices have revitalized barbiturases. Codon usage
patterns were analysed in this study for 17 barbiturase genes encoded by 16 bacterial species. Multivariate and correspondence study of amino acid and codon usage was employed for detecting the cause of variation in the
gene content. GC3 of synonymously variable codons,RSCU,NC and CAI were estimated with statistical softwares.
Examination of DNA composition along with codon usage was done to reveal dynamics of gene evolution and expression of this enzyme.
... Closely related species, living in distinct environments may exhibit considerable genomic diversity (Paul et al. 2010) that lead to differences in factors behind diversification of SCU patterns. Mutational pressure was found to be the major factor, influencing SCU pattern across PCG in strictly thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (Prabha et al. 2012) which is less adaptive to other temperature ranges as growth of thermophiles is restricted to particular environment at specific temperature (Botzman and Margalit 2011). These reports support our finding that SCU pattern of P. chromatophora and S. elongatus is dictated by mutational pressure due to their less adaptation to varying environments. ...
Comparative study of synonymous codon usage variations and factors influencing its diversification in α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301 has not been reported so far. In the present study, we investigated various factors associated with synonymous codon usage in the genomes of P. chromatophora and S. elongatus PCC6301 and findings were discussed.
Mutational pressure was identified as the major force behind codon usage variation in both genomes. However, correspondence analysis revealed that intensity of mutational pressure was higher in S. elongatus than in P. chromatophora. Living habitats were also found to determine synonymous codon usage variations across the genomes of P. chromatophora and S. elongatus.
Whole genome sequencing of α-cyanobacteria in the cyanobium clade would certainly facilitate the understanding of synonymous codon usage patterns and factors contributing its diversification in presumed ancestors of photosynthetic endosymbionts of P. chromatophora.
Invertebrate iridescent viruses (IIVs) are classified as double-stranded DNA viruses within the Iridoviridae family. IIVs are viruses that infect invertebrate hosts, causing symptoms that vary in intensity from slight reductions in host fitness to systemic disease. Numerous earlier investigations have provided insights into the genomic, proteomic, and transcriptional analyses of invertebrate iridescent viruses. However, the codon usage bias (CUB) of IIVs has yet to be fully understood. In order to gain a more profound insight into the evolutionary features of IIVs, we conducted an extensive analysis of the codon usage patterns in the DNA polymerase genes (DNA pol genes) of 12 invertebrate iridescent viruses. The analysis of both nucleotide composition and relative synonymous codon usage (RSCU) indicated a higher prevalence of AT-ended codons in the DNA pol genes of IIVs. Additionally, a low codon usage bias was determined from the effective number of codons (ENC) value. Analyses of ENC-GC3s plot, neutrality plot, and parity rule 2 plot illustrated that the codon usage patterns in IIVs DNA pol genes were influenced by both natural selection and mutational pressure. This investigation holds significance as it has delineated the codon usage patterns within the DNA pol genes of IIVs and has furnished crucial data for a foundational study of their evolutionary aspects.
Gynostemma plants are important Chinese medicinal material and economic crops. Codon usage analysis is a good way to understand organism evolution and phylogeny. There is no report yet about analysis of codon usage bias of chloroplast genomes in Gynostemma species. In this study, the chloroplast genomes in nine Gynostemma species were analyzed systematically to explore the factors affecting the formation of codon usage bias. The codon usage indicators were analyzed. Multivariate statistical analysis including analysis of neutrality plot, effective number of codons plot, parity rule 2 plot and correspondence were performed. Composition analysis of codons showed that the frequency of GC in chloroplast genes of all nine Gynostemma species was less than 50%, and the protein-coding sequences of chloroplast genes preferred to end with A/T at the third codon position. The chloroplast genes had an overall weak codon usage bias. A total of 29 high frequency codons and 12 optimal codons were identified. These could provide useful information in optimizing and modifying codons thus improving the gene expression of Gynostemma species. The results of multivariate analysis showed that the codon usage patterns were not only affected by single one factor but multiple factors. Mutation pressure, natural selection and base composition might have an influence on the codon usage patterns while natural selection might be the main determinant. The study could provide a reference for organism evolution and phylogeny of Gynostemma species and help to understand the patterns of codons in chloroplast genomes in other plant species.
Supplementary information:
The online version contains supplementary material available at 10.1007/s12298-021-01105-z.
The activities of NAIP Component-1 were
oriented towards capacity building in NARS for
adapting or response to the fast changing
requirements of research, technology development
and dissemination in the scenario of globalized
agriculture. The aim of the Component was mainly to
create a conducive environment that could ensure
better flow of knowledge, collaborations,
experimentations and implementation of innovations
in terms of (a) information, communication and
dissemination systems, (b) competitive business
planning and technology commercialization models,
(c) advance learning and state-of-the-art capacity
building initiatives, (d) value added market
intelligence services, (e) sound monitoring and
evaluation (M&E), and strengthened impact
evaluation systems, and (f) project friendly financial
management and procurement systems.
With the aim to create an enabling environment
for the management of change; to increase efficiency,
effectiveness and productivity of Indian NARS, the
objectives of Component-1 were addressed through
55 sub-projects distributed over five sub-components
namely; Information, Communication and Dissemination
System (22); Business Planning and Development
(23); Learning and Capacity Building (2); Policy,
Gender Analysis and Visioning (7), and Remodelling
Financial and Procurement Systems (1). The Project
Implementation Unit (PIU) of NAIP was also a part of
this component.
Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, β-herpes genes are common to β-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. β-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.
Different mechanisms regulate the expression level of tissue specific genes in human. Here we report some compositional features such as codon usage bias, amino acid usage bias, codon frequency, and base composition which may be potentially related to mRNA amount of tissue specific tumor suppressor genes. Our findings support the possibility that structural elements in gene and protein may play an important role in regulation of tumor suppressor genes, development, and tumorigenesis. The data presented here can open broad vistas in the understanding and treatment of a variety of human malignancies.
Stearoyl-acyl carrier protein desaturase (SAD) gene widely exists in all kinds of plants. In this paper, Camellia sinensis SAD gene (CsSAD) sequence was firstly analyzed by Codon W, CHIPS, and CUSP programs online, and then compared with genomes of tea plant, other species and SAD genes from 11 plant species. The results show that CsSAD gene and the selected 73 of C. sinensis genes have similar codon usage bias. CsSAD gene has a bias toward the synonymous codons with A and T at the third codon position, the same as the 73 of C. sinensis genes. Compared with monocotyledons such as Triticum aestivum and Zea mays, the differences in codon usage frequency between CsSAD gene and dicotyledons such as Arabidopsis thaliana and Nicotiana tobacum are less. Therefore, A. thaliana and N. tobacum expression systems may be more suitable for the expression of CsSAD gene. The analysis result of SAD genes from 12 plant species also shows that most of the SAD genes are biased toward the synonymous codons with G and C at the third codon position. We believe codon usage bias analysis presented in this study will be essential for providing a theoretical basis for discussing the structure and function of CsSAD gene.
