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

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.

Download Full-text

Comparative analysis of the codon usage patterns in two closely related Marsupenaeus species based on comparative transcriptomics

10.21203/rs.3.rs-88141/v1 ◽

2020 ◽

Author(s):

Panpan Wang ◽

Yong Mao ◽

Yongquan Su ◽

Jun Wang

Keyword(s):

Codon Usage ◽

Purifying Selection ◽

Evolutionary Trends ◽

Bias Analysis ◽

Codon Preference ◽

Plot Analysis ◽

Optimal Codons ◽

Traditional Classification ◽

Usage Patterns ◽

Codon Pairs

Abstract Background: Marsupenaeus japonicus, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Due to the lack of genomic information, little is known about the correlations among codon usage bias, gene expression, and evolutionary trends in Marsupenaeus orthologs.Results: Using the CodonW 1.4.2 software, we performed the codon bias analysis of two Marsupenaeus species transcriptomes. The average contents of GC and ENc were 51.61% and 52.1 for VI (M. japonicus), 51.54% and 52.22 for VII (M. pulchricaudatus), respectively. Parity Rule 2 (PR2) plot analysis showed that purines (A and G) were used more frequently than pyrimidines (C and T) in two Marsupenaeus species. The average ENc value was 52.1 and 52.22 for M. japonicus and M. pulchricaudatus, respectively. Overall, orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that experienced purifying selection (ω < 1). In M. japonicus, the relationships were highly significant positive about Axis 1 and A3, T3 and ENc (p < 0.01). However, all relationships in M. pulchricaudatus were the opposite. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively. Two Marsupenaeus species had 31 different codon pairs. The results of multi-species clustering based on codon preference were consistent with traditional classification. Conclusions: We characterized the codon usage patterns of the two Marsupenaeus species and the evolutionary trends in Marsupenaeus orthologs, which provides new insights into the genetic divergence and the phylogenetic relationships of two Marsupenaeus species.

Download Full-text

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.

Download Full-text

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.

Download Full-text

Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

10.21203/rs.3.rs-1125942/v1 ◽

2021 ◽

Author(s):

Yanan Fu ◽

Yanping Huang ◽

Jingjing Rao ◽

Feng Zeng ◽

Ruiping Yang ◽

...

Keyword(s):

Natural Selection ◽

Codon Usage ◽

Binding Affinity ◽

Codon Bias ◽

Synonymous Codon ◽

Host Adaptation ◽

Synonymous Codon Usage ◽

Mutation Pressure ◽

Usage Analysis ◽

Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

Download Full-text

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.

Download Full-text

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.

Download Full-text

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.

Download Full-text

Inferring biophysical models of evolution from genome-wide patterns of codon usage

10.1101/578815 ◽

2019 ◽

Author(s):

Willow B. Kion-Crosby ◽

Michael Manhart ◽

Alexandre V. Morozov

Keyword(s):

Population Genetics ◽

Codon Usage ◽

Codon Bias ◽

Purifying Selection ◽

Mutation Rates ◽

Nucleotide Position ◽

Mutational Robustness ◽

Translation Speed ◽

Genome Wide ◽

Speed And Accuracy

AbstractFrequencies of synonymous codons are typically non-uniform, despite the fact that such codons correspond to the same amino acid in the genetic code. This phenomenon, known as codon bias, is broadly believed to be due to a combination of factors including genetic drift, mutational biases, and selection for speed and accuracy of codon translation; however, quantitative modeling of codon bias has been elusive. We have developed a biophysical population genetics model which explains genome-wide codon frequencies observed across 20 organisms. We assume that codons evolve independently of each other under the influence of mutation and selection forces, and that the codon population has reached evolutionary steady state. Our model implements codon-level treatment of mutations with transition/transversion biases, and includes two contributions to codon fitness which describe codon translation speed and accuracy. Furthermore, our model includes wobble pairing – the possibility of codon-anticodon base pairing mismatches at the 3’ nucleotide position of the codon. We find that the observed patterns of genome-wide codon usage are consistent with a strong selective penalty for mistranslated amino acids. Thus codons undergo purifying selection and their relative frequencies are affected in part by mutational robustness. We find that the dependence of codon fitness on translation speed is weaker on average compared to the strength of selection against mistranslation. Although no constraints on codon-anticodon pairing are imposed a priori, a reasonable hierarchy of pairing rates, which conforms to the wobble hypothesis and is consistent with available structural evidence, emerges spontaneously as a model prediction. Finally, treating the translation process explicitly in the context of a finite ribosomal pool has allowed us to estimate mutation rates per nucleotide directly from the coding sequences. Reminiscent of Drake’s observation that mutation rates are inversely correlated with the genome size, we predict that mutation rates are inversely proportional to the number of genes. Overall, our approach offers a unified biophysical and population genetics framework for studying codon bias across all domains of life.

Download Full-text

Codon Usage Bias of the Wheat Flower Development Gene WAG-2 and Other AGAMOUS Group Genes

Journal of Agricultural Science ◽

10.5539/jas.v9n9p56 ◽

2017 ◽

Vol 9 (9) ◽

pp. 56

Author(s):

Wenhan Hu ◽

Shuhong Wei

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Codon Bias ◽

Target Genes ◽

Expression System ◽

Functional Studies ◽

Codon Preference ◽

Synonymous Codons ◽

The Difference ◽

Relationship Of

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.

Download Full-text

Analysis of Codon Usage Pattern and Predicted Gene Expression in Neurospora Crassa: A Novel in Silico Approach

International Journal of Pharma and Bio Sciences ◽

10.22376/ijpbs/lpr.2021.11.5.l35-60 ◽

2021 ◽

Vol 11 (5) ◽

Author(s):

Sahoo Satyabrata

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Neurospora Crassa ◽

Codon Bias ◽

Genomic Structure ◽

Regulation Of Gene Expression ◽

Codon Usage Pattern ◽

Mrna Levels ◽

Usage Pattern ◽

Promising Alternative

The codon usage pattern of genes has a key role in the gene expression and adaptive evolution of an organism. It is very significant in understanding the role of complex genomic structure in defining cell fates and regulating diverse biological functions. In this paper, we discussed that the codon usage index (CAIg) based on all protein-coding genes is a promising alternative to the Codon Adaptation Index (CAI). CAIg which measures the extent that a gene uses a subset of preferred codons relies exclusively on sequence features and is used as a good indicator of the strength of codon bias. A critical analysis of predicted highly expressed (PHE) genes in Neurospora crassa has been performed using codon usage index (CAIg) as a numerical estimator of gene expression level. Analyzing compositional properties and codon usage pattern of genes in Neurospora crassa, our study indicates that codon composition plays an important role in the regulation of gene expression. We found a systematic strong correlation between CAIg and CBI (codon bias index) or other expression-measures. Here, we show that codon usage index CAIg correlates well with both protein and mRNA levels; suggesting that codon usage is an important determinant of gene expression. Our study highlights the relationship between gene expression and compositional signature in relation to codon usage bias in Neurospora crassa and sets the ground for future investigation in eukaryotic biology.

Download Full-text