Deciphering Codon Usage Patterns in Genome of Cucumis sativus in Comparison with Nine Species of Cucurbitaceae

Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbitaceae on the genomic level. The analysis of fundamental indicators of codon characteristics shows that it was slightly GC poor, and there was weak codon usage bias in cucumber. We conduct the analysis of neutrality plot, ENC plot, P2 index, and COA indicates that the nucleotide composition, mutation pressure, and translational selection might play roles in CUB in cucumber and its relatives. Among these factors, nucleotide composition might play the most critical role. Based on these analyses, 30 optimal codons were identified in cucumber, most of them ending with U or A. Meanwhile, based on the RSCU values of species, a cluster tree was constructed, in which the situation of cucumber is consistent with the current taxonomic and evolutionary studies in Cucurbitaceae. This study systematically compared the CUB patterns and shaping factors of cucumber and its relatives, laying a foundation for future research on genetic engineering and evolutionary mechanisms in Cucurbitaceae.

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Analysis of synonymous codon usage of transcriptome database in Rheum palmatum

PeerJ ◽

10.7717/peerj.10450 ◽

2021 ◽

Vol 9 ◽

pp. e10450

Author(s):

Xiaowei Huo ◽

Sisi Liu ◽

Yimin Li ◽

Hao Wei ◽

Jing Gao ◽

...

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Synonymous Codon ◽

Expression System ◽

Evolutionary Mechanisms ◽

Mutation Pressure ◽

Rheum Palmatum ◽

Optimal Codons

Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.

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Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19

Biomolecules ◽

10.3390/biom11060912 ◽

2021 ◽

Vol 11 (6) ◽

pp. 912

Author(s):

Saadullah Khattak ◽

Mohd Ahmar Rauf ◽

Qamar Zaman ◽

Yasir Ali ◽

Shabeen Fatima ◽

...

Keyword(s):

Standard Deviation ◽

Codon Usage ◽

Codon Usage Bias ◽

Geographic Location ◽

Mutation Pressure ◽

Genome Wide ◽

Margin Of Error ◽

Usage Patterns ◽

Causative Agents ◽

Virus Genomes

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons’ A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome’s level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.

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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Genes ◽

10.3390/genes12081169 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1169

Author(s):

Xin Li ◽

Xiaocen Wang ◽

Pengtao Gong ◽

Nan Zhang ◽

Xichen Zhang ◽

...

Keyword(s):

Codon Usage ◽

Genetic Manipulation ◽

Molecular Genetic ◽

Gc Content ◽

Giardia Duodenalis ◽

Codon Usage Pattern ◽

Protein Size ◽

New Genes ◽

Optimal Codons ◽

Usage Patterns

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

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Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

10.1101/2021.03.03.433699 ◽

2021 ◽

Author(s):

Neetu Tyagi ◽

Rahila Sardar ◽

Dinesh Gupta

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Gc Content ◽

Respiratory Illness ◽

Respiratory Viruses ◽

Nucleotide Composition ◽

Health Crisis ◽

Study Results ◽

Usage Patterns ◽

The Difference

AbstractThe Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

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Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species

PeerJ ◽

10.7717/peerj.8251 ◽

2020 ◽

Vol 8 ◽

pp. e8251 ◽

Cited By ~ 1

Author(s):

Zhanjun Wang ◽

Beibei Xu ◽

Bao Li ◽

Qingqing Zhou ◽

Guiyi Wang ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Comparative Analysis ◽

Codon Usage ◽

Plant Species ◽

Populus Trichocarpa ◽

Model Organisms ◽

Mutation Pressure ◽

Chloroplast Genomes ◽

Usage Patterns ◽

Exogenous Expression

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

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

Viruses ◽

10.3390/v11121087 ◽

2019 ◽

Vol 11 (12) ◽

pp. 1087 ◽

Cited By ~ 2

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.

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

Viruses ◽

10.3390/v11040331 ◽

2019 ◽

Vol 11 (4) ◽

pp. 331 ◽

Cited By ~ 8

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.

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Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family

Australian Journal of Botany ◽

10.1071/bt12073 ◽

2012 ◽

Vol 60 (5) ◽

pp. 461 ◽

Cited By ~ 10

Author(s):

Yuerong Zhang ◽

Xiaojun Nie ◽

Xiaoou Jia ◽

Cunzhen Zhao ◽

Siddanagouda S. Biradar ◽

...

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Mutational Bias ◽

Plot Analysis ◽

Optimal Codons ◽

Chloroplast Genomes ◽

Usage Patterns ◽

Poaceae Family ◽

High Representation

Codon usage patterns of 23 Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations with GC12 and GC3 and also showed strong bias towards a high representation of NNA and NNT codons. The Nc-plot showed that although a large proportion of points follow the parabolic line of trajectory, several genes with low ENc values lie below the expected curve, suggesting that mutational bias played a major role in the codon biology of the Poaceae chloroplast genome. Parity Rule 2 plot analysis showed that T was used more frequently than A in all the genomes. Correspondence analysis of relative synonymous codon usage indicated that the first axis explained only a partial amount of variation of codon usage. Furthermore, the gene length and expression level were also found to drive codon usage variation. These findings revealed that besides natural selection, other factors might also exert some influences in shaping the codon usage bias in Poaceae chloroplast genomes. The optimal codons of these 23 genomes were also identified in this study.

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Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific

Viruses ◽

10.3390/v10110604 ◽

2018 ◽

Vol 10 (11) ◽

pp. 604 ◽

Cited By ~ 15

Author(s):

Naveen Kumar ◽

Diwakar Kulkarni ◽

Benhur Lee ◽

Rahul Kaushik ◽

Sandeep Bhatia ◽

...

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Similarity Index ◽

Hendra Virus ◽

Human Beings ◽

Mutation Pressure ◽

Usage Patterns ◽

Adaptation Index

Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation in different hosts is lacking. A study of codon usage patterns in henipaviruses may provide some fruitful insight into their evolutionary processes of synonymous codon usage and host-adapted evolution. Here, we performed a systematic evolutionary and codon usage bias analysis of henipaviruses. We found a low codon usage bias in the coding sequences of henipaviruses and that natural selection, mutation pressure, and nucleotide compositions shapes the codon usage patterns of henipaviruses, with natural selection being more important than the others. Also, henipaviruses showed the highest level of adaptation to bats of the genus Pteropus in the codon adaptation index (CAI), relative to the codon de-optimization index (RCDI), and similarity index (SiD) analyses. Furthermore, a comparison to recently identified henipa-like viruses indicated a high tRNA adaptation index of henipaviruses for human beings, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in human beings, particularly when paired with frequent exposure to direct/indirect bat excretions.

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Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Viruses ◽

10.3390/v12090991 ◽

2020 ◽

Vol 12 (9) ◽

pp. 991

Author(s):

Huiguang Wu ◽

Zhengyu Bao ◽

Chunxiao Mou ◽

Zhenhai Chen ◽

Jingwen Zhao

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Synonymous Codon ◽

Similarity Index ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Broad Host Range ◽

Mutation Pressure ◽

Porcine Astrovirus ◽

Usage Patterns

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

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