Codon bias (codon preference, codon usage bias)

Analyzing codon usage bias of WAG-2 gene in wheat three-pistil (TP) mutant may provide a basis for selecting the appropriate host expression systems to improve the expression of target genes. In the present study, we analyzed the codon bias of the complete coding sequence (CDS) of the WAG-2 gene in TP using Codon W program, and compared the results with AGAMOUS (AG) group genes of other plant species. Results showed that the WAG-2 gene in TP and other monocot AG group genes preferably used codons ending with G/C bases, but Arabidopsis thaliana, Nicotiana tabacum, and other dicot crops were biased toward the synonymous codons with A/T. The clustering results based on codon bias were consistent with those based on CDS of the AG group genes, indicating that the difference in codon preference of AG group genes sequences was closely associated with the genetic relationship of the species. The Euclidean distance coefficients of WAG-2 with A. thaliana and N. tabacum were 9.255 and 5.730, respectively, indicating that N. tabacum may be more suitable for the expression of WAG-2. There were 37 codons showing distinct usage differences between WAG-2 and genome of yeast, 23 between WAG-2 and Escherichia coli. Therefore, the E. coli was the superior protein expression system. These results may improve our understanding of codon usage bias and functional studies of WAG-2.

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Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus

Marine Drugs ◽

10.3390/md18090464 ◽

2020 ◽

Vol 18 (9) ◽

pp. 464

Author(s):

Xinjia Li ◽

Wanyi Chen ◽

Dongting Zhangsun ◽

Sulan Luo

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Major Type ◽

Snail Species ◽

Cone Snail ◽

Codon Preference ◽

Specific Receptors ◽

Marine Peptide ◽

Simple Sequence ◽

Repeat Detection

The venom of various Conus species is composed of a rich variety of unique bioactive peptides, commonly referred to as conotoxins (conopeptides). Most conopeptides have specific receptors or ion channels as physiologically relevant targets. In this paper, high-throughput transcriptome sequencing was performed to analyze putative conotoxin transcripts from the venom duct of a vermivorous cone snail species, Conus litteratus native to the South China Sea. A total of 128 putative conotoxins were identified, most of them belonging to 22 known superfamilies, with 43 conotoxins being regarded as belonging to new superfamilies. Notably, the M superfamily was the most abundant in conotoxins among the known superfamilies. A total of 15 known cysteine frameworks were also described. The largest proportion of cysteine frameworks were VI/VII (C-C-CC-C-C), IX (C-C-C-C-C-C) and XIV (C-C-C-C). In addition, five novel cysteine patterns were also discovered. Simple sequence repeat detection results showed that di-nucleotide was the major type of repetition, and the codon usage bias results indicated that the codon usage bias of the conotoxin genes was weak, but the M, O1, O2 superfamilies differed in codon preference. Gene cloning indicated that there was no intron in conotoxins of the B1- or J superfamily, one intron with 1273–1339 bp existed in a mature region of the F superfamily, which is different from the previously reported gene structure of conotoxins from other superfamilies. This study will enhance our understanding of conotoxin diversity, and the new conotoxins discovered in this paper will provide more potential candidates for the development of pharmacological probes and marine peptide drugs.

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Codon Usage Bias in Two Hemipteran Insect Species: Bemisia tabaci and Homalodisca coagulata

Advances in Biology ◽

10.1155/2014/145465 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Jyotika Sharma ◽

Supriyo Chakraborty ◽

Arif Uddin

Keyword(s):

Codon Usage ◽

Bemisia Tabaci ◽

Codon Usage Bias ◽

Codon Bias ◽

Insect Species ◽

Codon Usage Pattern ◽

Mutation Pressure ◽

Homalodisca Coagulata ◽

Highly Expressed Genes ◽

Hemipteran Insect

Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species.

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Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

BMC Genomics ◽

10.1186/s12864-021-08106-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Panpan Wang ◽

Yong Mao ◽

Yongquan Su ◽

Jun Wang

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Codon Bias ◽

Purifying Selection ◽

Marsupenaeus Japonicus ◽

Bias Analysis ◽

Codon Preference ◽

Optimal Codons ◽

Usage Patterns ◽

Usage Analysis

Abstract Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

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Entropy and codon bias in HIV-1

10.1101/052274 ◽

2016 ◽

Author(s):

Aakash Pandey

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Nucleotide Composition ◽

Threshold Values ◽

Minimum Entropy ◽

Maximum Information ◽

Human Genes ◽

Efficient Expression ◽

Hiv 1

AbstractFor the heterologous gene expression systems, the codon bias has to be optimized according to the host for efficient expression. Although DNA viruses show a correlation on codon bias with their hosts, HIV genes show low correlation for both nucleotide composition and codon usage bias with its human host which limits the efficient expression of HIV genes. Despite this variation, HIV is efficient at infecting hosts and multiplying in large number. In this study, first, the degree of codon adaptation is calculated as codon adaptation index (CAI) and compared with the expected threshold value (eCAI) determined from the sequences with the same nucleotide composition as that of the HIV-1 genome. Then, information theoretic analysis of nine genes of HIV-1 based on codon statistics of the HIV-1 genome, individual genes and codon usage of human genes is done. Comparison of codon adaptation indices with their respective threshold values shows that the CAI lies very close to the threshold values. Despite not being well adapted to the codon usage bias of human hosts, it was found that the Shannon entropies of the nine genes based on overall codon statistics of HIV-1 genome are very similar to the entropies calculated from codon usage of human genes. Similarly, for the HIV-1 genome sequence analyzed, the codon statistics of the third reading frame has the highest bias representing minimum entropy and hence the maximum information.

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Enhanced effective codon numbers to understand codon usage bias

10.1101/644609 ◽

2019 ◽

Cited By ~ 1

Author(s):

Reginald Smith

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Driving Forces ◽

Relative Strength ◽

Relative Influence ◽

New Method ◽

Different Types

AbstractCodon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the relative strength of each of these forces and how genes or organisms have their codon biases shaped. In particular, it demonstrates that variation in codon usage bias across organisms is likely driven more by mutational forces while the variation in codon usage bias within genomes is likely driven by selectional forces.Author summaryA new method of disaggregating codon bias influences (G+C content, mutational biases, and selection) is described where I show how that different values of the effective codon number, following Wright’s Nc, can be used as ratios to demonstrate the similar or different causes of codon biases across genes or organisms. By calculating ratios of the different types of effective codon numbers, one can easily compare organisms or different genes while controlling for G+C content or relative mutational biases. The driving forces determining the variations in codon usage bias across or within organisms thus become much clearer.

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The Correlation Between Synonymous and Nonsynonymous Substitutions in Drosophila: Mutation, Selection or Relaxed Constraints?

Genetics ◽

10.1093/genetics/150.2.767 ◽

1998 ◽

Vol 150 (2) ◽

pp. 767-775 ◽

Cited By ~ 9

Author(s):

Josep M Comeron ◽

Martin Kreitman

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Nonsynonymous Substitution ◽

Synonymous Substitution ◽

Synonymous Change ◽

Replacement Substitution ◽

Synonymous And Nonsynonymous Substitutions ◽

Codon Family ◽

Preferred Codon

Abstract Codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including Drosophila, yeast, and many bacteria. Preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. In Drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon usage in genes with high codon bias than in genes with low codon bias. Surprisingly, in these organisms, as well as in mammals, the rate of synonymous substitution is also positively correlated with the rate of nonsynonymous substitution. To investigate this correlation, we carried out a phylogenetic analysis of substitutions in 22 genes between two species of Drosophila, Drosophila pseudoobscura and D. subobscura, in codons that differ by one replacement and one synonymous change. We provide evidence for a relative excess of double substitutions in the same species lineage that cannot be explained by the simultaneous mutation of two adjacent bases. The synonymous changes in these codons also cannot be explained by a shift to a more preferred codon following a replacement substitution. We, therefore, interpret the excess of double codon substitutions within a lineage as being the result of relaxed constraints on both kinds of substitutions in particular codons.

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Evolution of Codon Usage Bias in Diatoms

Genes ◽

10.3390/genes10110894 ◽

2019 ◽

Vol 10 (11) ◽

pp. 894 ◽

Cited By ~ 1

Author(s):

Marc Krasovec ◽

Dmitry A. Filatov

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Diatom Species ◽

Effective Population ◽

Weak Selection ◽

Optimal Codons ◽

Wide Range ◽

Population Sizes ◽

Selection For

Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process—frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.

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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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Codon usage bias in radioresistant bacteria

10.1101/2020.02.25.964916 ◽

2020 ◽

Author(s):

Maddalena Dilucca ◽

Athanasia Pavlopoulou ◽

Alexandros G. Georgakilas ◽

Andrea Giansanti

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Trna Gene ◽

Gene Copy Number ◽

Gene Copy ◽

Mutational Bias ◽

Gene Copies ◽

Control Set ◽

The Relationship

AbstractThe relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.

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