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

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.

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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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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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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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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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Comprehensive analysis of codon usage pattern of whole genome in protozoa, Stylonychia lemnae

10.21203/rs.2.16499/v1 ◽

2019 ◽

Author(s):

ying wang ◽

Lin Yao ◽

Jinfeng Fan ◽

Xueying Zhang ◽

Changhong Guo ◽

...

Keyword(s):

Codon Usage ◽

Classical Model ◽

Mrna Translation ◽

Codon Usage Pattern ◽

Translational Efficiency ◽

Usage Pattern ◽

Evolutionary Origins ◽

Plot Analysis ◽

Two Factors ◽

Usage Patterns

Abstract Background: Codon usage pattern is an important evolutionary feature in genomes widely observed in many organisms. Stylonychia lemnae is a classical model single-celled eukaryote, and a quintessential ciliate typified by dimorphic nuclei: a germline micronucleus and a vegetative macronucleus. Analysis of codon usage pattern of S. lemnae macronucleus genome helps in understanding evolution at molecular level and acquires signiﬁcance in mRNA translation, design of transgenic and new gene discovery. Results: The codons of the macronucleus genome sequence of S. lemnae were analyzed and 20,750 coding sequences (CDS) were screened. The overall codon usage of S. lemnae is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in S. lemnae is relatively high. Nucleotide analysis showed that the overall codon usage is biased toward A- and U-ending codons. The phylogenetic analysis indicated that ciliate is independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of S. lemnae is more similar to that of Thtrahymana thermophila and Paramecium caudatum . Correlation analysis, ENC-GC 3S plot, and PR2 plot indicated that the codon usage patterns of S. lemnae are influenced by both mutational pressure and natural selection, neutrality plot analysis showed that those two factors play major roles. C onclusions : Codon usage patterns in eukaryotes are not determined by translational efficiency, but also are determined by the genome. Our study is the ﬁrst attempt to evaluate the codon usage pattern of S.lemnae macronucleus genome to better understand the evolutionary changes. These results built the base for further research on the molecular evolution of S. lemnae .

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Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints

PeerJ ◽

10.7717/peerj.10787 ◽

2021 ◽

Vol 9 ◽

pp. e10787

Author(s):

Huirong Duan ◽

Qian Zhang ◽

Chunmei Wang ◽

Fang Li ◽

Fuping Tian ◽

...

Keyword(s):

Codon Usage ◽

Driving Forces ◽

Gc Content ◽

Pressure Effects ◽

Perennial Herb ◽

Evolutionary Analysis ◽

Plot Analysis ◽

Optimal Codons ◽

Mapping Analysis ◽

Cp Genome

Background Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC3 content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection. Discussions Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.

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Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species

PLoS ONE ◽

10.1371/journal.pone.0020083 ◽

2011 ◽

Vol 6 (5) ◽

pp. e20083 ◽

Cited By ~ 12

Author(s):

Jane E. Stewart ◽

Masato Kawabe ◽

Zaid Abdo ◽

Tsutomu Arie ◽

Tobin L. Peever

Keyword(s):

Codon Usage ◽

Purifying Selection ◽

Fungal Species ◽

Usage Patterns

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Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2023575118 ◽

2021 ◽

Vol 118 (20) ◽

pp. e2023575118

Author(s):

Shakibur Rahman ◽

Sergei L. Kosakovsky Pond ◽

Andrew Webb ◽

Jody Hey

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Purifying Selection ◽

Synonymous Substitution ◽

Weak Selection ◽

Codon Model ◽

Synonymous Substitutions ◽

Synonymous Codons ◽

Usage Patterns

Synonymous codon substitutions are not always selectively neutral as revealed by several types of analyses, including studies of codon usage patterns among genes. We analyzed codon usage in 13 bacterial genomes sampled from across a large order of bacteria, Enterobacterales, and identified presumptively neutral and selected classes of synonymous substitutions. To estimate substitution rates, given a neutral/selected classification of synonymous substitutions, we developed a flexible dN/dS substitution model that allows multiple classes of synonymous substitutions. Under this multiclass synonymous substitution (MSS) model, the denominator of dN/dS includes only the strictly neutral class of synonymous substitutions. On average, the value of dN/dS under the MSS model was 80% of that under the standard codon model in which all synonymous substitutions are assumed to be neutral. The indication is that conventional dN/dS analyses overestimate these values and thus overestimate the frequency of positive diversifying selection and underestimate the strength of purifying selection. To quantify the strength of selection necessary to explain this reduction, we developed a model of selected compensatory codon substitutions. The reduction in synonymous substitution rate, and thus the contribution that selection makes to codon bias variation among genes, can be adequately explained by very weak selection, with a mean product of population size and selection coefficient, Ns=0.8.

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Identification of the optimal codons for acetolactate synthase from weeds: an in-silico study

Plant Soil and Environment ◽

10.17221/562/2020-pse ◽

2021 ◽

Author(s):

Madhab Kumar Sen ◽

Kateřina Hamouzová ◽

Sunil Kanti Mondal ◽

Josef Soukup

Keyword(s):

Codon Usage ◽

Herbicide Resistance ◽

Codon Usage Bias ◽

Target Genes ◽

Acetolactate Synthase ◽

Resistance Evolution ◽

Optimal Codons ◽

In Silico Study ◽

Usage Patterns ◽

New Compounds

Although various studies of codon usage bias have been reported in a broad spectrum of organisms, no studies to date have examined codon usage bias for herbicide target genes. In this study, we analysed codon usage patterns for the acetolactate synthase (ALS) gene in eight monocot weeds and one model monocot. The base composition at the third codon position follows C3 > G3 > T3 > A3. The values of the effective number of codons (ENC or Nc) indicate low bias, and ENC or Nc vs. GC3 plot suggests that this low bias is due to mutational pressure. Low codon adaptation index and codon bias index values further supported the phenomenon of low bias. Additionally, the optimal codons, along with over- and under-represented codons, were identified. Gene design using optimal codons rather than overall abundant codons produce improved protein expression results. Our results can be used for further studies, including eliciting the mechanisms of herbicide resistance (occurring due to elevation of gene expression levels) and the development of new compounds, their efficiency and risk assessment for herbicide resistance evolution.

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