Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Liu, H; Huang, Yubi; Du, Xianghong; Chen, Z; Zeng, Xing; Chen, Y; Zhang, H

doi:10.4238/2012.october.17.3

Cited by 28 publications

(30 citation statements)

References 37 publications

(56 reference statements)

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“…Although a small number of genes distributed in the vicinity of the expected curve, indicated that compositional constraint was the only determinant factor shaping the codon usage pattern. A majority of genes with low ENC values deviated well below the expected curve, indicating that GC3s value was a major determinant of codon usage bias and that other factors independent of nucleotide composition shaped codon usage as well [65]. Consequently, the codon usage pattern of genes in the four cotton genomes and the four subgenomes might be shaped by the combined effects of directional mutation and neutral selection.…”

Section: Enc and Gc3s Scatter Plot (Enc-plot)mentioning

confidence: 88%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

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Section: Enc and Gc3s Scatter Plot (Enc-plot)mentioning

confidence: 88%

Genome-wide analysis of codon usage bias in four sequenced cotton species

et al. 2018

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“…If the distribution of the plotted genes is below the curve, then the codon usage bias is assumed to be affected by selection and other factors (Liu et al, 2012).…”

Section: Enc-gc3 Plotmentioning

confidence: 99%

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Khodary

Anwar

2020

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In the present study, we analyzed genome-wide codon usage patterns in 13 SARS-CoV-2 isolates from different geo-locations (countries) by utilizing different CUB measurements. Nucleotide and di-nucleotide compositions displayed bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Relative Synonymous Codon Usage (RSCU) analysis revealed 8 common putative preferred codons among all the 13 isolates.Interestingly, all of the latter codons are A/U-ended (U-ended: 7, A-ended: 1). Cluster analysis (based on RSCU values) was performed and showed comparable results to the phylogenetic analysis (based on their whole genome sequences) indicating that the CUB pattern may reflect the evolutionary relationship between the tested isolates. To investigate the force (mutation and/or selection) influencing the pattern of CUB in SARS-CoV-2 coding sequences, we employed the following; (i). Effective number of codons (ENc), (ii). ENc-GC3 plot, (iii). Neutrality plot, and (iv) Codon adaptation index (CAI). According to their results, natural selection and/or other factors (not investigated in this study) may be the dominant force driving SARS-CoV-2 CUB. It is also worth mentioning that, by using the most expressed genes in human lung tissues as a reference set, some viral genes such as Nucleocapsid phosphoprotein, ORF7a protein, and surface glycoprotein had high CAI values which may indicate for selection force acting on their codon usage, as they play important roles in viral assembly and may help viruses avoid the host immune system. The outcome of our study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 viruses, and the interactions with their host. Also, it may aid in vaccine design strategies.

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“…We found a reasonable pattern of evolutionary relationships between the LjNBS genes. Most researchers have identified two clades of NBS genes in dicots, TIR-type and non-TIR-type genes (Liu et al, 2012). However, research in monocots has been unable to resolve relationships among NBS domain sequences, and has yielded a star-like topology (Cheng et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

“…The average GC3s value was 0.38, indicating a high frequency of AT in LjNBS gene sequences at the third position. Reduced selection against mutations in plant genomes could lead to a wide distribution bias of GC3s values (Liu et al, 2012). In LjNBS genes, the GC3s values ranged from 0.29 to 0.54, suggesting that LjNBS genes underwent mutation pressure or selection against mutation.…”

Section: Codon Usage Bias In L Japonicus Nbs-encoding Genesmentioning

confidence: 99%

Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

Song

Wang

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Nucleotide-binding site (NBS) disease resistance genes play a crucial role in plant defense responses against pathogens and insect pests. Many NBS-encoding genes have been detected in Lotus japonicus, an important forage crop in many parts of the world. However, most NBS genes identified so far in L. japonicus were only partial sequences. We identified 45 full-length NBS-encoding genes in the L. japonicus genome, and analyzed gene duplications, motifs, and the molecular phylogeny to further understand the NBS gene family. We found that gene duplication events rarely occur in L. japonicus NBS-encoding (LjNBS) genes. In addition, LjNBS genes were subjected to selection pressure, and codon usage bias was evident. We tested for purifying selection (specifically in the CC-NBS-LRR and TIR-NBS-LRR groups), and found strong purifying selection in the TIR-domain-containing sequences, indicating that the CC-NBS-LRR group is more likely to undergo expansion than the TIR-NBS- LRR group. Moreover, our results showed that both selection and mutation contributed to LjNBS codon usage bias, but mutational bias was the major influence on codon usage.

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Patterns of synonymous codon usage bias in the model grass Brachypodium distachyon

Cited by 28 publications

References 37 publications

Genome-wide analysis of codon usage bias in four sequenced cotton species

Genome-wide analysis of codon usage bias in four sequenced cotton species

Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

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