Oxford University Press eBooks · 2012
Abstract Codon-based models of evolution are a relatively new addition to the toolkit of computational biologists, and in recent years remarkable progress has been made in this area. The study of evolution at the codon level captures information contained in both amino acid and synonymous DNA substitutions. By combining these two types of information, codon analyses are more powerful than those of either amino acid or DNA evolution alone. This is a clear benefit for most evolutionary analyses, including phylogenetic reconstruction, detection of selection, ancestral sequence reconstruction, and alignment of coding DNA. Despite the theoretical advantages of codon-based models, their relative complexity delayed their widespread use. Only in recent years, when large-scale sequencing projects produced sufficient genomic data and computational power increased, did their usage become more common. This book provides the latest insights from codon-based analyses of genetic sequences. The first part of the book provides comprehensive coverage of the developments of various types of codon-substitution models such as parametric and empirical models used in maximum likelihood as well as Bayesian frameworks. Subsequent chapters examine the use of codon models to infer selection and other applications of codon models to biological systems. The second part of the book focuses on codon usage bias. Both the underlying mechanisms as well as current methods to analyse codon usage bias are presented.
Cited by 32
Syozo Osawa, Thomas H. Jukes · Journal of Molecular Evolution · 1989
Cited by 291
Hiroshi Akashi (35384), Piyush Goel (35385), Anoop John (35386) · Figshare · 2015
<p>Trees representing extant codon configurations consistent with single silent changes in the <i>m</i> lineage, ECC_uppppp (A) and ECC_puuuuu (E), are shown. The three most common ancestral codon configurations underlying these extant codon configurations are shown in B, C, and D for ECC_uppppp and in E, F, and G for ECC_puuuuu. Trees C and G reflect child/ancestor reverse changes and trees D and H show child/sib-ancestor parallel changes. The relative frequencies of ancestral codon configurations underlying ECC_uppppp and ECC_puuuuu in the codon bias simulations are shown as bubble plots beneath the trees. The sizes of the bubbles reflect the relative numbers of ancestral codon configurations in each class for three different MCU values. For the non-equilibrium scenarios (1/3<i>N</i><sub>e</sub> and 2<i>N</i><sub>e</sub>), the proportion of each ancestral codon configuration among the extant configurations relative to the proportion under equilibrium codon bias evolution are given. The data are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001065#pone-0001065-t001" target="_blank">Table 1</a>.</p>
Cited by 0Open access
Ginés Rivas, Juan José · University of Huddersfield Repository (University of Huddersfield) · 2021
The emergence of life on Earth developed a system of DNA containing the information inherited in the reproduction of organisms, directing also the variability of life as this changes. The language using for deciphering the DNA is the genetic code, which is degenerated as 20 amino acids are codified by 64 codons, or triplets of nitrogenous bases (adenine, guanine, cytosine and thymine) in the nucleotides that form the DNA. 59 codons have other/s synonymous codons, and those are not used randomly but are a product of different phenomena. The drivers of codon usage bias can be mutations, genetic drift and natural selection processes. The study of these codons can provide evolutionary information, like gene family evolution and organisation, can offer an insight in population size, and also can be used to create software to predict ORFs and coding regions. Codon study also can be important in biotechnology for heterologous expression, as the codon used have a control over the efficiency and accuracy during translation, resulting in determinant for protein folding, growth rate and avoidance of defective proteins. Opisthokonta is a group of organisms, close to Apusomonadida, and gathering Holozoa (Ichthyosporea, Filasterea, Choanoflagellatea and Metazoa) and Holomycota. The present study uses the transcriptome of 20 choanoflagellates species, Sphaeroforma arctica (Class Ichthyosporea), Thecamonas trahens (class Apusomonadea) and five early branching metazoans (Amphimedon queenslandica, Mnemiopsis leidyi, Nematostella vectensis, Thelohanellus kitauei and Trichoplax adhaerens) to study the codon usage bias and anticodon related phenomena in the mentioned species. Analysis revealed optimal codons for each organism, with a GC ended codons enrichment in T. trahens, unicellular Opisthokonta, and retained after the transition to pluricellularity (with divergences in M. leidyi and N. vectensis). All the unicellular species showed evidence for natural selection upon translational accuracy and efficiency, even the less biased ones. In metazoan only translational efficiency was evidenced, with lower strength of selection, and poor support for translational accuracy in ctenophoran and cnidarian species. For other strategies giving advantages on protein translation, indirect evidence of deamination in high degenerated amino acids was found in all the species studied, while direct evidence was found in S. arctica, A. queenslandica, M. leidyi and N. vectensis. Additionally, tRNA presenting isotype-anticodon disagreements were found in apusomonadean, ichthyosporean, metazoan species and in S. rosetta. Deamination, and possibly chimeric tRNA appeared early in evolution, before the divergence of Apusomonadea and Opisthokonta, benefiting the use of optimal codons through evolution until the apparition of the latest metazoan organisms.
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Paul M. Sharp, Giorgio Matassi · Current Opinion in Genetics & Development · 1994
Cited by 253
Juan Jose Gines Rivas · Figshare · 2022
The folder contains the scripts, predicted proteins, CDS, ncRNA, DNA toplevel files and expression levels used in the PhD thesis "Codon Usage Evolution in Opisthokonta".<br>Author: Juan José Ginés RivasMain Supervisor: Dr Martin Carr<br>
Cited by 0Open access
Ian Henry · Nottingham ePrints (University of Nottingham) · 2007
Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing codon usage within this genome to be related to translational selection. The relationship between the degree of codon\nusage adaptation (as given by the ‘frequency of optimal codons’ statistic) and putative gene expression level was used to look for genes with unusually high or low expression levels in B. bacteriovorus, in comparison to Escherichia coli, in order to gain further insight into the unusual lifestyle of this Delta Proteobacterium.\n\nThe scope was then broadened to explore intergenomic patterns of codon usage and initially extend a study measuring the strength of selected codon usage bias across bacterial genomes (Sharp et al. 2005). A dataset of 160 fully sequenced bacterial genomes was used and the strength of selected codon usage bias was seen to vary greatly between species. A correlation was observed between (log of) generation time and the strength of selected codon usage bias with fast growing bacteria showing a higher degree of selected codon usage bias than slow growing bacteria.\n\nIn bacterial species exhibiting significant levels of selected codon usage bias optimal codon choice was examined. It was observed that optimal codon choice is not always conserved across all bacterial genomes under selection but broad trends in optimal codon choice were seen to be associated with particular bacterial clades. In general, optimal codon choice was seen to be linked with differences in mutational biases among the clades, as seen by a correlation between optimal codon choice in particular clades and the G+C content of their genomes. Clades that were A+U rich (Firmicutes, Gamma Proteobacteria main clade) were seen to largely prefer codons of the form NNA/U whilst G+C rich clades (Alpha Proteobacteria, Actinobacteria and Xanthomonas species) showed preference for codons of the form NNG/C in their highly expressed genes.\n\nFinally the relationship between optimal codon usage and tRNA abundances was explored. Changes in tRNA abundances were seen to coincide with switches in optimal codon usage. Therefore, switches in codon usage and tRNA abundance are thought to be influenced by changing mutational bias within the genome as reflected by the correlation between optimal codon choice, tRNA gene complements and genomic G+C content.
Cited by 2Open access
Jianzhi Zhang · Genetics · 2004
Volatility of a codon is defined as the probability that a random point mutation in the codon generates a nonsynonymous change. It has been proposed that higher-than-expected mean codon volatility of a gene indicates that positive selection for nonsynonymous changes has acted on the gene in the recent past. I show that strong frequency-dependent selection (minority advantage) in large populations can increase codon volatility slightly, whereas directional positive selection has no effect on volatility. Factors unrelated to positive selection, such as expression-related or GC-content-related codon usage bias, also affect volatility. These and other considerations suggest that codon volatility has only limited utility for detecting positive selection at the DNA sequence level.
Cited by 29Open access
Gines Rivas, Juan Jose · Figshare · 2022
The folder contains the scripts, predicted proteins, CDS, ncRNA, DNA toplevel files and expression levels used in the PhD thesis "Codon Usage Evolution in Opisthokonta".<br>Author: Juan José Ginés RivasMain Supervisor: Dr Martin Carr<br>
Cited by 0Open access
Fang-Ping Wang, Hong Li · Gene · 2008
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Davenport, J Bernard · OpenGrey (Institut de l'Information Scientifique et Technique) · 2004
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Adam Eyre‐Walker · ERA · 1992
A new statistical test has been developed to detect selection on silent sites.This test compares the codon usage within a gene and thus does not require knowledge of which genes are under the greatest selection, that there exist common trends in codon usage across genes, or that genes have the same mutation pattern.It also controls for mutational biases that might be introduced by the adjacent bases.The test was applied to 62 mammalian sequences, and significant codon usage biases were detected in all three species examined (humans, rats, and mice).However, these biases appear not to be the consequence of selection, but of the first base pair in the codon influencing the mutation pattern at the third position.
Cited by 2Open access
Premal R Shah · 2011
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H Green, N Wang · Proceedings of the National Academy of Sciences · 1994
Sequence data banks have been searched for proteins possessing uninterrupted reiterations of any amino acid. Hydrophilic amino acids, and particularly glutamine, account for a large proportion of the longer reiterants. In the genes for these proteins, the most common reiterants are those that contain poly(CAG), even out-of-frame or, to a lesser degree, those that contain repeated doublets of CA, AG, or GC. The preferential generation of such reiterants requires that DNA strand-specific signals predispose to reiteration and thus to the extension of coding regions.
Cited by 91Open access
Daniel T. Wright · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign) · 2011
The informational properties of biological systems are the subject of much \ndebate and research. I present a general argument in favor of the existence \nand central importance of information in organisms, followed by a case study \nof the genetic code (specifically, codon bias) and the translation system from \nthe perspective of information. The codon biases of 831 Bacteria and Archeae \nare analyzed and modeled as points in a 64-dimensional statistical space. The \nmajor results are that (1) codon bias evolution does not follow canonical \npatterns, and (2) the use of coding space in organsims is a subset of the \ntotal possible coding space. These findings imply that codon bias is a unique \nadaptive mechanism that owes its existence to organisms' use of information in \nrepresenting genes, and that there is a particularly biological \ncharacter to the resulting biased coding and information use.
Cited by 0
Laurent Duret · Current Opinion in Genetics & Development · 2002
Cited by 512
Marc Krasovec, Dmitry A. Filatov · Genes · 2019
Codon usage bias (CUB)-preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as <i>Drosophila</i> that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (<i>N</i><sub>e</sub>), with fluctuations in population size and linked selection limiting long-term <i>N</i><sub>e</sub> and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in <i>Skeletonema marinoi</i> corresponds to <i>N</i><sub>e</sub> of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, <i>N</i><sub>e</sub> ~10<sup>7</sup> should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process-frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3<sup>rd</sup> codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most <i>Chaetoceros</i> species, while for <i>Chaetoceros dichaeta</i> GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.
Cited by 16Open access
David A. McClellan · Journal of Molecular Evolution · 2000
Cited by 43
Morozov, Alexandre V. · TIB KMO / FLOWWORKS GmbH · 2019
Frequencies 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 effects, and selection for speed and accuracy of codon translation; however, quantitative modeling of codon bias has been somewhat elusive. I will present a biophysical model which explains genome-wide codon frequencies observed across 20 organisms. Our model implements detailed codon-level treatment of mutations and includes two contributions to codon fitness which describe codon translation speed and accuracy. We find that the observed patterns of genome-wide codon usage are consistent with a strong selective penalty for mistranslated amino acids, while the dependence of codon fitness on translation speed is much weaker on average. Treating the translation process explicitly in the context of a finite ribosomal pool has allowed us to highlight the biophysical underpinnings of codon-level selective pressures. Overall, our approach offers a unified biophysical and population genetics framework for understanding the origin of codon bias.
Cited by 0Open access
Joel Osuna · Nucleic Acids Research · 2004
A method to delete in-phase codons throughout a defined target region of a gene has been developed. This approach, named the codon-based random deletion (COBARDE) method, is able to delete complete codons in a random and combinatorial mode. Robustness, automation and fine-tuning of the mutagenesis rate are essential characteristics of the method, which is based on the assembly of oligonucleotides and on the use of two transient orthogonal protecting groups during the chemical synthesis. The performance of the method for protein function evolution was demonstrated by changing the substrate specificity of TEM-1 beta-lactamase. Functional ceftazidime-resistant beta-lactamase variants containing several deleted residues inside the catalytically important omega-loop region were found. The results show that the COBARDE method is a useful new molecular tool to access previously unexplorable sequence space.
Cited by 23Open access