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

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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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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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 Bias in Mitochondrial Genome of Epinephelus Fuscoguttatus

10.21203/rs.3.rs-590314/v1 ◽

2021 ◽

Author(s):

Lirong Bai ◽

Lili Lu ◽

Suping Li ◽

Jicui He ◽

Jian Chen ◽

...

Keyword(s):

Mitochondrial Genome ◽

Codon Usage ◽

Codon Bias ◽

Synonymous Codon ◽

Economic Value ◽

Gc Content ◽

Optimal Codons ◽

Epinephelus Fuscoguttatus ◽

The Difference ◽

Usage Preference

Abstract Background: Epinephelus fuscoguttatus is one of the rare marine economic fishes with high economic value. At present, the researches on grouper mainly focus on artificial propagation, physiology and biochemistry, diseases and so on. However, there are few reports on mitochondrial genome level. The research aimed to analyze composition characteristics and usage preference of codon of mitochondrial genome in E. fuscoguttatus, and explored main factors of affecting the formation of codon preference, thereby providing theoretical basis for studying species evolution, genetics and breeding, and improving expression efficiency of exogenous genes. Results: GC content of mitochondrial genome of E. fuscoguttatus changed between 44.00% and 46.30%, with 45.40% of mean. Change range of CAI value was between 0.125 and 0.202, and the mean was 0.155. Effective number of codons (ENC) changed between 36.08 and 49.55, with 44.98 of mean. There were 32 codons that relative synonymous codon usage (RSCU) was more than 1, mainly ended with A/C. ENC-plot analysis found that all the genes were in the lower middle of the standard curve, and there was larger difference between actual and theoretical ENC, illustrating that codon bias was mainly affected by the choice. Correspondence analysis showed that the first axis contributed 58.85% of the difference, while the second, third and fourth axes contributed 14.59%, 7.66% and 5.43% of the difference respectively. Cumulative contribution rate of the first four vectors was 85.53%. Finally, nine optimal codons were selected: CUU, AUC, GUU, CCU, GCA, UAU, CGC, AGC and GGC.Conclusions: Codon usage preference of mitochondrial genome of E. fuscoguttatus was weak, and it preferred to use A/C terminated codon, and preference was mainly influenced by choice.

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Analysis of codon usage bias reveals optimal codons in Elaeis guineensis

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211138 ◽

2020 ◽

Vol 21 (11) ◽

Author(s):

Redi Aditama ◽

Zulfikar Achmad Tanjung ◽

Widyartini Made Sudania ◽

Yogo Adhi Nugroho ◽

Condro Utomo ◽

...

Keyword(s):

Codon Usage ◽

Oil Palm ◽

Codon Usage Bias ◽

Elaeis Guineensis ◽

Synonymous Codon ◽

Gc Content ◽

Synonymous Codon Usage ◽

Mutational Bias ◽

Optimal Codons ◽

Good Ability

Abstract. Aditama R, Tanjung ZA, Sudania WM, Nugroho YA, Utomo C, Liwang T. 2020. Analysis of codon usage bias reveals optimal codons in Elaeis guineensis. Biodiversitas 21: 5331-5337. Codon usage bias of oil palm genome was reported employing several indices, including GC content, relative synonymous codon usage (RSCU), the effective number of codons (ENC), and codon adaptation index (CAI). Unimodal distribution of GC content was observed and matched with non-grass monocots characteristics. Correspondence analysis (COA) on synonymous codon usage bias showed that the main axis was strongly driven by GC content. The ENC and neutrality plot of oil palm genes indicating that natural selection played more vital role compared to mutational bias on shaping codon usage bias. A positive correlation between calculated CAI and experimental data of oil palm gene expression was detected indicating good ability of this index. Finally, eighteen codons were defined as “optimal codons” that may provide a useful reference for heterogeneous expression and genome editing studies.

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Elucidation of Codon Usage Signatures across the Domains of Life

10.1101/421487 ◽

2018 ◽

Author(s):

Eva Maria Novoa ◽

Olivier Jaillon ◽

Irwin Jungreis ◽

Manolis Kellis

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Codon Usage Bias ◽

Gc Content ◽

Single Amino Acid ◽

Common Belief ◽

Domain Specific ◽

Optimal Codons ◽

A Genome ◽

Domains Of Life

AbstractDue to the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being ‘synonymous’, these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is generally attributed to mutational drift, is the major determinant of interspecies codon usage bias. Here we find that in addition to the bias caused by GC content, inter-species codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding, and show that the identified domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain with high accuracy. Considering that species belonging to the same domain share similar tRNA decoding strategies, we then wondered whether the inclusion of codon autocorrelation patterns might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to the common belief. Instead, our results reveal that codon autocorrelation patterns are a consequence of codon optimality throughout a sequence, where highly expressed genes display autocorrelated ‘optimal’ codons, whereas lowly expressed genes display autocorrelated ‘non-optimal’ codons.

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Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

10.21203/rs.3.rs-99464/v1 ◽

2020 ◽

Author(s):

Hui-rong Duan ◽

Qian Zhang ◽

Hongshan Yang ◽

Fuping Tian ◽

Yu Hu ◽

...

Keyword(s):

Codon Usage ◽

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Genomic Structure ◽

Native Plant ◽

Coding Regions ◽

Evolution Analysis ◽

Optimal Codons ◽

Related Plant ◽

Cp Genome

Abstract BackgroundThe perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.ResultsThe cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identiﬁed. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.ConclusionsOur results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

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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.

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Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

10.21203/rs.3.rs-49271/v1 ◽

2020 ◽

Author(s):

Huirong Duan ◽

Qian Zhang ◽

Hongshan Yang ◽

Fuping Tian ◽

Yu Hu ◽

...

Keyword(s):

Codon Usage ◽

Adaptive Evolution ◽

Phylogenetic Relationships ◽

Genomic Structure ◽

Native Plant ◽

Coding Regions ◽

Evolution Analysis ◽

Optimal Codons ◽

Related Plant ◽

Cp Genome

Abstract Background The perennial shrub of Calligonum mongolicum is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.Results The cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identified. Synonymous codon usage (SCU) analysis exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.Conclusions Our results comprehensively depicts the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.

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Elucidation of Codon Usage Signatures across the Domains of Life

Molecular Biology and Evolution ◽

10.1093/molbev/msz124 ◽

2019 ◽

Vol 36 (10) ◽

pp. 2328-2339 ◽

Cited By ~ 11

Author(s):

Eva Maria Novoa ◽

Irwin Jungreis ◽

Olivier Jaillon ◽

Manolis Kellis

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Gc Content ◽

Classification Performance ◽

Single Amino Acid ◽

Domain Specific ◽

Optimal Codons ◽

A Genome ◽

Highly Expressed Genes ◽

Domains Of Life

Abstract Because of the degeneracy of the genetic code, multiple codons are translated into the same amino acid. Despite being “synonymous,” these codons are not equally used. Selective pressures are thought to drive the choice among synonymous codons within a genome, while GC content, which is typically attributed to mutational drift, is the major determinant of variation across species. Here, we find that in addition to GC content, interspecies codon usage signatures can also be detected. More specifically, we show that a single amino acid, arginine, is the major contributor to codon usage bias differences across domains of life. We then exploit this finding and show that domain-specific codon bias signatures can be used to classify a given sequence into its corresponding domain of life with high accuracy. We then wondered whether the inclusion of codon usage codon autocorrelation patterns, which reflects the nonrandom distribution of codon occurrences throughout a transcript, might improve the classification performance of our algorithm. However, we find that autocorrelation patterns are not domain-specific, and surprisingly, are unrelated to tRNA reusage, in contrast to previous reports. Instead, our results suggest that codon autocorrelation patterns are a by-product of codon optimality throughout a sequence, where highly expressed genes display autocorrelated “optimal” codons, whereas lowly expressed genes display autocorrelated “nonoptimal” codons.

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Genome-wide characterization and identification of synonymous codon usage patterns in Plasmodium knowlesi

10.1101/2021.01.01.425038 ◽

2021 ◽

Author(s):

Manoj Kumar Yadav ◽

Shivani Gajbhiye

Keyword(s):

Codon Usage ◽

Plasmodium Knowlesi ◽

Sequence Data ◽

Synonymous Codon ◽

Gc Content ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Optimal Codons ◽

Usage Patterns

AbstractCodon usage bias is a ubiquitous phenomenon occurring at both, interspecies and intraspecies level in different organisms. P. knowlesi, whose natural host is long-tailed Macaque monkeys, has recently started infecting humans as well. The genome as well as coding sequence data of P. knowlesi is used to understand their codon usage pattern in the light of other human infecting Plasmodium species: P. vivax and P. falciparum. The different codon usage indicators: GC content, relative synonymous codon usage, effective number of codon and codon adaptation index are studied to analyze codon usage in the Plasmodium species. The codon usage pattern is found to be less conserved in studied Plasmodium species, and changes species to species at the genus level. The codon usage pattern of P. knowlesi shows similarity to P. vivax as compared to P. falciparum. The ENC vs. GC3 study indicates that compositional constraints and translation selection is the decisive forces responsible for shaping their codon usage. The studies Plasmodium species shows a higher usage of A/T ending optimal codons. This favors the codon bias in P. knowlesi and P. vivax is due to high selection pressure and in P. falciparum, the compositional mutational pressure is a dominant force. In a nutshell, our finding suggests that the more or less similar codon usage pattern of P. knowlesi and P. vivax may suggest the similar host invasion and immune evasion strategies for disease establishment.

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