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1.
Susanta K. Behura David W. Severson 《Biological reviews of the Cambridge Philosophical Society》2013,88(1):49-61
Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole‐genome sequencing of numerous species, both prokaryotes and eukaryotes, genome‐wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole‐genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome‐sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome‐sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. 相似文献
2.
Oscar E. R. Lehmann Martín D. Ezcurra Richard J. Butler Graeme T. Lloyd 《Palaeontology》2019,62(5):837-849
The Generalized Euclidean Distance (GED) measure has been extensively used to conduct morphological disparity analyses based on palaeontological matrices of discrete characters. This is in part because some implementations allow the use of morphological matrices with high percentages of missing data without needing to prune taxa for a subsequent ordination of the data set. Previous studies have suggested that this way of using the GED may generate a bias in the resulting morphospace, but a detailed study of this possible effect has been lacking. Here, we test whether the percentage of missing data for a taxon artificially influences its position in the morphospace, and if missing data affects pre‐ and post‐ordination disparity measures. We find that this use of the GED creates a systematic bias, whereby taxa with higher percentages of missing data are placed closer to the centre of the morphospace than those with more complete scorings. This bias extends into pre‐ and post‐ordination calculations of disparity measures and can lead to erroneous interpretations of disparity patterns, especially if specimens present in a particular time interval or clade have distinct proportions of missing information. We suggest that this implementation of the GED should be used with caution, especially in cases with high percentages of missing data. Results recovered using an alternative distance measure, Maximum Observed Rescaled Distance (MORD), are more robust to missing data. As a consequence, we suggest that MORD is a more appropriate distance measure than GED when analysing data sets with high amounts of missing data. 相似文献
3.
Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986 相似文献
4.
In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum likelihood-ratio tests to compare the performance of two models, one in which a single codon is overrepresented and one in which two codons are overrepresented. The measure allowed us to analyze both the extent of bias in each lineage and the evolution of codon choice across the phylogeny. Despite predictions based primarily on the low G+C content of the chloroplast and the high functional importance of rbcL, we found large differences in the extent of bias, suggesting differential molecular selection that is clade specific. The seed plants and simple leafy liverworts each independently derived a low level of bias in rbcL, perhaps indicating relaxed selectional constraint on molecular changes in the gene. Overrepresentation of a single codon was typically plesiomorphic, and transitions to overrepresentation of two codons occurred commonly across the phylogeny, possibly indicating biochemical selection. The total codon bias in each taxon, when regressed against the total bias of each amino acid, suggested that twofold amino acids play a strong role in inflating the level of codon usage bias in rbcL, despite the fact that twofolds compose a minority of residues in this gene. Those amino acids that contributed most to the total codon usage bias of each taxon are known through amino acid knockout and replacement to be of high functional importance. This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness.
Present address (Joshua T. Herbeck): JBP Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA 相似文献
5.
6.
Sophie Marion de Procé Daniel L. Halligan Peter D. Keightley Brian Charlesworth 《Journal of molecular evolution》2009,69(6):601-611
Contrary to the classical view, a large amount of non-coding DNA seems to be selectively constrained in Drosophila and other
species. Here, using Drosophila miranda BAC sequences and the Drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between D. pseudoobscura and D. miranda, and investigated their patterns of evolution. We found two patterns that have previously been observed in comparisons between
Drosophila melanogaster and its relatives. First, there is a negative correlation between intron divergence and intron length, suggesting that longer
non-coding sequences may contain more regulatory elements than shorter sequences. Our other main finding is a negative correlation
between the rate of non-synonymous substitutions (d
N) and codon usage bias (F
op), showing that fast-evolving genes have a lower codon usage bias, consistent with strong positive selection interfering with
weak selection for codon usage. 相似文献
7.
Despite the degeneracy of the genetic code, whereby different codons encode the same amino acid, alternative codons and amino acids are utilized nonrandomly within and between genomes. Such biases in codon and amino acid usage have been demonstrated extensively in prokaryote genomes and likely reflect a balance between the action of mutation, selection, and genetic drift. Here, we quantify the effects of selection and mutation drift as causes of codon and amino acid-usage bias in a large collection of nematode partial genomes from 37 species spanning approximately 700 Myr of evolution, as inferred from expressed sequence tag (EST) measures of gene expression and from base composition variation. Average G + C content at silent sites among these taxa ranges from 10% to 63%, and EST counts range more than 100-fold, underlying marked differences between the identities of major codons and optimal codons for a given species as well as influencing patterns of amino acid abundance among taxa. Few species in our sample demonstrate a dominant role of selection in shaping intragenomic codon-usage biases, and these are principally free living rather than parasitic nematodes. This suggests that deviations in effective population size among species, with small effective sizes among parasites, are partly responsible for species differences in the extent to which selection shapes patterns of codon usage. Nevertheless, a consensus set of optimal codons emerges that is common to most taxa, indicating that, with some notable exceptions, selection for translational efficiency and accuracy favors similar sets of codons regardless of the major codon-usage trends defined by base compositional properties of individual nematode genomes. 相似文献
8.
Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: Codon usage,map position,and concerted evolution 总被引:14,自引:0,他引:14
Paul M. Sharp 《Journal of molecular evolution》1991,33(1):23-33
Summary The nature and extent of DNA sequence divergence between homologous proteincoding genes fromEscherichia coli andSalmonella typhimurium have been examined. The degree of divergence varies greatly among genes at both synonymous (silent) and nonsynonymous sites. Much of the variation in silent substitution rates can be explained by natural selection on synonymous codon usage, varying in intensity with gene expression level. Silent substitution rates also vary significantly with chromosomal location, with genes nearoriC having lower divergence. Certain genes have been examined in more detail. In particular, the duplicate genes encoding elongation factor Tu,tufA andtufB, fromS. typhimurium have been compared to theirE. coli homologues. As expected these very highly expressed genes have high codon usage bias and have diverged very little between the two species. Interestingly, these genes, which are widely spaced on the bacterial chromosome, also appear to be undergoing concerted evolution, i.e., there has been exchange between the loci subsequent to the divergence of the two species.Presented at the NATO Advanced Research Workshop on Genome Organization and Evolution, held in Spetses, Greece, September 1990 相似文献
9.
The actinorhizal genusAlnus contains numerous taxa that have been morphologically classified into different subgenera, species and subspecies. The genetic divergence has been evaluated within subg.Alnobetula between the parapatric taxaAlnus sinuata andA. crispa, using diversity of allozyme markers at 15 structural loci among 20 populations. Evidence for introgressive hybridization at the overlap of their ranges was noted in three populations. However, the width of the hybrid zone appeared tenuous. The average genetic distance derived from the comparisons of conspecific populations was much smaller than the interspecific distance (D = 0.047). This allelic divergence was also paralleled with larger amounts of allelic and genotypic diversity within and among populations ofA. sinuata, which are occupying a more heterogenous ecological niche. It is proposed that the repeated advances and retreats of the ice sheet during the Pleistocene may have promoted the divergence and allopatric evolution of these subspecies, and that secondary contact may have occurred repeatedly during the interglacial periods. The dynamic-equilibrium model would predict in such cases that narrow hybrid zones, formed at the contact of parapatric ranges, would impede gene exchange between parental taxa by selection against hybrids. The results obtained in this study seemed concordant with this hypothesis, as they were also in agreement with the existent taxonomical treatment of these taxa based on morphology. 相似文献
10.
Codon usage and base composition in sequences from the A + T-rich genome ofRickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among
genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational
selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according
to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition
patterns of 21R. prowazekii proteins with that of a homologous set of proteins fromEscherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding
proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions
have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests thatR. prowazekii has around 800 genes and that 60–70% of the genome may be coding.
Correspondence to: S.G.E. Andersson 相似文献
11.
Christianson ML 《American journal of botany》2005,92(8):1221-1233
12.
Francesco Frati Chris Simon Jack Sullivan David L. Swofford 《Journal of molecular evolution》1997,44(2):145-158
The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic
levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic
relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all
insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the
basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions
appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in
some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels
observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or
exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity
of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information
was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical
support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well
supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from
an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.
Received: 12 January 1996 / Accepted: 10 August 1996 相似文献
13.
Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide
choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures.
In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding
first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform
to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that
genes from different genomes can be separated with a high degree of accuracy, according to these distance values.
In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their
poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides,
we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects.
Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene
present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking
correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.
Received: 16 January 2001 / Accepted: 30 August 2001 相似文献
14.
Background
Codon usage bias (CUB), the uneven use of synonymous codons, is a ubiquitous observation in virtually all organisms examined. The pattern of codon usage is generally similar among closely related species, but differs significantly among distantly related organisms, e.g., bacteria, yeast, and Drosophila. Several explanations for CUB have been offered and some have been supported by observations and experiments, although a thorough understanding of the evolutionary forces (random drift, mutation bias, and selection) and their relative importance remains to be determined. The recently available complete genome DNA sequences of twelve phylogenetically defined species of Drosophila offer a hitherto unprecedented opportunity to examine these problems. We report here the patterns of codon usage in the twelve species and offer insights on possible evolutionary forces involved. 相似文献15.
Background
Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patterns reflect the effects of positive Darwinian selection acting at the level of translational efficiency or whether these patterns are due simply to the effects of mutational bias. In this study, we have included both intra-genomic and inter-genomic comparisons of codon usage. This allows us to distinguish more efficiently between the effects of nucleotide bias and translational selection.Results
We show that there is an extreme degree of heterogeneity in codon usage patterns within the rice genome, and that this heterogeneity is highly correlated with differences in nucleotide content (particularly GC content) between the genes. In contrast to the situation observed within the rice genome, Arabidopsis genes show relatively little variation in both codon usage and nucleotide content. By exploiting a combination of intra-genomic and inter-genomic comparisons, we provide evidence that the differences in codon usage among the rice genes reflect a relatively rapid evolutionary increase in the GC content of some rice genes. We also noted that the degree of codon bias was negatively correlated with gene length.Conclusion
Our results show that mutational bias can cause a dramatic evolutionary divergence in codon usage patterns within a period of approximately two hundred million years.The heterogeneity of codon usage patterns within the rice genome can be explained by a balance between genome-wide mutational biases and negative selection against these biased mutations. The strength of the negative selection is proportional to the length of the coding sequences. Our results indicate that the large variations in synonymous codon usage are not related to selection acting on the translational efficiency of synonymous codons.16.
Comparative Analysis of Codon Usage Patterns Among Mitochondrion, Chloroplast and Nuclear Genes in Triticum aestivum L. 总被引:4,自引:0,他引:4
Wen-Juan Zhang Jie Zhou Zuo-Feng Li Li Wang Xun Gu Yang Zhong 《植物学报(英文版)》2007,49(2):246-254
In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat (Triticum aestivum L.). GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 (PR2) plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints. 相似文献
17.
Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome. 相似文献
18.
Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. 总被引:12,自引:0,他引:12
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Synonymous codon usage varies considerably among Caenorhabditis elegans genes. Multivariate statistical analyses reveal a single major trend among genes. At one end of the trend lie genes with relatively unbiased codon usage. These genes appear to be lowly expressed, and their patterns of codon usage are consistent with mutational biases influenced by the neighbouring nucleotide. At the other extreme lie genes with extremely biased codon usage. These genes appear to be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. Thus, the frequency of these optimal codons in a gene appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels (or even function) are unknown. A second, relatively minor trend among genes is correlated with the frequency of G at synonymously variable sites. It is not yet clear whether this trend reflects variation in base composition (or mutational biases) among regions of the C.elegans genome, or some other factor. Sequence divergence between C.elegans and C.briggsae has also been studied. 相似文献
19.
文中对子囊菌代表类群的延伸因子1 alpha基因密码子的使用模式进行了研究。结果表明:该基因的密码子使用偏好性不仅与核酸碱基组成密切相关,也受到其他选择性压力的影响。统计分析揭示了子囊菌各类群该基因的密码子组成和编码特点,在同义密码子的选择模式上,酵母纲(Saccharomycetes)的成员具有较独特的偏好性。基于密码子用法分歧度的聚类分析方法较合理地反映了大部分类群的分类学地位,但在各个纲的内部,密码子偏好性的变化程度存在差异。 相似文献
20.
Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes 总被引:1,自引:0,他引:1