Codon usage and base composition inRickettsia prowazekii

1996 ◽  
Vol 42 (5) ◽  
pp. 525-536 ◽  
Author(s):  
Siv G. E. Andersson ◽  
Paul M. Sharp
Keyword(s):  
Codon Usage ◽  
Base Composition

scholarly journals Selection on silent sites in the rodent H3 histone gene family.

Genetics ◽  
1994 ◽  
Vol 138 (1) ◽  
pp. 191-202
Author(s):  
R W DeBry ◽  
W F Marzluff
Keyword(s):  
Codon Usage ◽  
Gene Conversion ◽  
Base Composition ◽  
Large Scale ◽  
Synonymous Codon ◽  
Histone Genes ◽  
Flanking Sequence ◽  
Effective Population ◽  
Mutation Pressure ◽  
Synonymous Codons

Abstract Selection promoting differential use of synonymous codons has been shown for several unicellular organisms and for Drosophila, but not for mammals. Selection coefficients operating on synonymous codons are likely to be extremely small, so that a very large effective population size is required for selection to overcome the effects of drift. In mammals, codon-usage bias is believed to be determined exclusively by mutation pressure, with differences between genes due to large-scale variation in base composition around the genome. The replication-dependent histone genes are expressed at extremely high levels during periods of DNA synthesis, and thus are among the most likely mammalian genes to be affected by selection on synonymous codon usage. We suggest that the extremely biased pattern of codon usage in the H3 genes is determined in part by selection. Silent site G + C content is much higher than expected based on flanking sequence G + C content, compared to other rodent genes with similar silent site base composition but lower levels of expression. Dinucleotide-mediated mutation bias does affect codon usage, but the affect is limited to the choice between G and C in some fourfold degenerate codons. Gene conversion between the two clusters of histone genes has not been an important force in the evolution of the H3 genes, but gene conversion appears to have had some effect within the cluster on chromosome 13.

scholarly journals Hill–Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret

2003 ◽  
Vol 81 (2) ◽  
pp. 89-90 ◽  
Author(s):  
RICHARD M. KLIMAN ◽  
JODY HEY
Keyword(s):  
Drosophila Melanogaster ◽  
Codon Usage ◽  
Recombination Rate ◽  
Base Composition ◽  
Potential Role ◽  
Compositional Bias ◽  
Stochastic Effects ◽  
Protein Coding ◽  
Biasing Effects ◽  
Preferred Codon

The usage of preferred codons in Drosophila melanogaster is reduced in regions of lower recombination. This is consistent with population genetics theory, whereby the effectiveness of selection on multiple targets is limited by stochastic effects caused by linkage. However, because the selectively preferred codons in D. melanogaster end in C or G, it has been argued that base-composition-biasing effects of recombination can account for the observed relationship between preferred codon usage and recombination rate (Marais et al., 2003). Here, we show that the correlation between base composition (of protein-coding and intron regions) and recombination rate holds only for lower values of the latter. This is consistent with a Hill–Robertson interference model and does not support a model whereby the entire effect of recombination on codon usage can be attributed to its potential role in generating compositional bias.

scholarly journals Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes

2021 ◽  
Author(s):  
Brian R. Morton
Keyword(s):  
Codon Usage ◽  
Significant Role ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Context Effects ◽  
Chloroplast Genes ◽  
Mutation Bias ◽  
Highly Expressed Genes ◽  
Context Dependent ◽  
Mutation Dynamics

AbstractTwo competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between the observed and expected codon usage when context effects are taken into consideration, with psbA being a notable exception. Overall, the data support the model that selection is not a widespread factor affecting the codon usage of angiosperm chloroplast genes and highlight the need to have an accurate model of mutational dynamics.

Schistosoma mansoni: patterns of codon usage and bias

Parasitology ◽  
1995 ◽  
Vol 110 (1) ◽  
pp. 53-60 ◽  
Author(s):  
J. T. Ellis ◽  
D. A. Morrison
Keyword(s):  
Multidimensional Scaling ◽  
Schistosoma Mansoni ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Significant Heterogeneity ◽  
Metric Multidimensional Scaling

Codon usage and bias has been examined in 20 genes ofSchistosoma mansoni. Significant heterogeneity was detected in the patterns of codon usage and bias among genes by metric multidimensional scaling and three general indictors of bias (GC3S, Ncand B). In keeping with observations on sporozoan parasites, codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were over or under-represented in the sequences.

scholarly journals Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts

2021 ◽  
Vol 12 ◽  
Author(s):  
Diego Simón ◽  
Juan Cristina ◽  
Héctor Musto
Keyword(s):  
Codon Usage ◽  
Dna Sequences ◽  
Base Composition ◽  
Genetic Material ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Double Stranded Dna ◽  
Causative Agents ◽  
Domains Of Life ◽  
Living Organisms

The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

Comparison of base composition and codon usage in insect mitochondrial genomes

2009 ◽  
Vol 31 (1) ◽  
pp. 65-71 ◽  
Author(s):  
Zheng Sun ◽  
Dong-Guang Wan ◽  
Robert W Murphy ◽  
Liang Ma ◽  
Xian-Sheng Zhang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Base Composition ◽  
Mitochondrial Genomes

scholarly journals Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Viruses ◽  
2013 ◽  
Vol 5 (1) ◽  
pp. 162-181 ◽  
Author(s):  
Daniel Cardinale ◽  
Kate DeRosa ◽  
Siobain Duffy
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Plant Viruses ◽  
Translational Selection

Codon usage and bias among individual genes of the coccidia and piroplasms

Parasitology ◽  
1994 ◽  
Vol 109 (3) ◽  
pp. 265-272 ◽  
Author(s):  
J. T. Ellis ◽  
D. A. Morrison ◽  
D. Avery ◽  
A. M. Johnson
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Base Composition ◽  
Gene Sequences ◽  
Parasitic Protozoa ◽  
Mutation Pressure ◽  
Individual Gene ◽  
Usage Patterns ◽  
Directional Mutation Pressure ◽  
The Individual

SummaryCodon usage has been analysed in individual gene sequences, derived from a variety of parasitic protozoa in the class Sporozoa of the phylum Apicomplexa using metric multidimensional scaling. The two groups of codon usage patterns detected reflect the two main subgroups of organisms studied (the coccidia and the piroplasms), and it is the pattern usage of synonymous codons that has the largest influence on overall codon usage in the individual genes, rather than being the pattern of amino acid composition of the gene product. The magnitude of the codon usage bias in the sequences was determined using three commonly used indices – NC', GC3sand B. In general, although relatively low levels of codon usage bias were detected in these gene sequences, codon usage bias does explain at least some of the codon usage patterns observed. Codon usage bias was observed to be dependent on the overall base composition of the genes analysed, which in turn was reflected in the types of codons that were either over-or under-represented in the nucleotide sequences. keeping with observations on prokaryotic organisms, it is speculated that the codon usage patterns detected in these parasitic protozoa are the result of directional mutation pressure on the base composition of the genomic DNA.

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