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1.
Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family 总被引:1,自引:0,他引:1
Xiaojun Nie Pingchuan Deng Kewei Feng Peixun Liu Xianghong Du Frank M You Song Weining 《Plant Molecular Biology Reporter》2014,32(4):828-840
Codon usage bias (CUB) is an important evolutionary feature in a genome and has been widely documented from prokaryotes to eukaryotes. However, the significance of CUB in the Asteraceae family has not been well understood, with no Asteraceae species having been analyzed for this characteristic. Here, we use bioinformatics approaches to comparatively analyze the general patterns and influencing factors of CUB in five Asteraceae chloroplast (cp) genomes. The results indicated that the five genomes had similar codon usage patterns, showing a strong bias towards a high representation of NNA and NNT codons. Neutrality analysis showed that these cp genomes had a narrow GC distribution and no significant correlation was observed between GC12 and GC3. Parity Rule 2 (PR2) plot analysis revealed that purines were used more frequently than pyrimidines. Effective number of codons (ENc)-plot analysis showed that most genes followed the parabolic line of trajectory, but several genes with low ENc values lying below the expected curve were also observed. Furthermore, correspondence analysis of relative synonymous codon usage (RSCU) yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggested that both natural selection and mutational bias contributed to codon bias, while selection was the major force to shape the codon usage in these Asteraceae cp genomes. Our study, which is the first to investigate codon usage patterns in Asteraceae plastomes, will provide helpful information about codon distribution and variation in these species, and also shed light on the genetic and evolutionary mechanisms of codon biology within this family. 相似文献
2.
Rahul R Nair Manivasagam B Nandhini Elango Monalisha Kavitha Murugan Thilaga Sethuraman Sangeetha Nagarajan Nayani Surya Prakash Rao Doss Ganesh 《Bioinformation》2012,8(22):1096-1104
Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find
out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as
chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz.,
leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A3, T3,
G3, C3, GC3) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast
genome. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve
indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the
continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional
constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents.
Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation
of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined
with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica. 相似文献
3.
4.
Matsuo Y 《Molecular phylogenetics and evolution》2000,15(2):283-291
The nucleotide divergence in the protein-coding region for replication-dependent and replication-independent histone 3 and 4 genes of Drosophila melanogaster and Drosophila hydei occurred mostly at the synonymous site. Therefore, the pattern of codon usage was analyzed in the two species, considering the genomic codon bias, which is proposed for estimating the genomic composition pressure in the protein-coding regions. The results indicated that the codon usage in the histone gene family could be explained mostly by the genomic codon bias. However, biases for Ala and Arg were commonly observed for the histone 3 and histone 4 gene families, and biases for Ser, Leu, and Glu were observed in a gene-specific manner. This suggests that both genomic codon bias and gene- or codon-specific bias are responsible for the nucleotide differentiation in the protein-coding region of the histone genes. 相似文献
5.
Comparative analysis of expansin gene codon usage patterns among eight plant species 总被引:1,自引:0,他引:1
Hao Zhang Jian Li Ruixue Wang Junkai Zhi Peng Yin 《Journal of biomolecular structure & dynamics》2019,37(4):910-917
Expansins are essential components of plant cell wall and play an important role in plant growth, development, and stress resistance via loosening function. To understand the codon usage pattern of expansin genes, we gained the sequence data of expansin genes from eight plant species. Statistics analysis showed obvious codon characteristics between monocot and dicot plants. Comparably, expansin genes in monocot plants had really higher GC content, more high-frequency codons, and more optimal codons than that in dicot plants. Several monocot plants performed somehow as dicot plants in a few characters. Codon information of expansin genes might contribute to the understanding of the relationship and evolution clues between monocot and dicot plants. It further gained insight into the improvement of the gene expression and roles. 相似文献
6.
Xinxin Wang Liang Wu Ping Zhou Shengfeng Zhu Wei An Yu Chen Lin Zhao 《World journal of microbiology & biotechnology》2013,29(11):2015-2024
The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman’s rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium. 相似文献
7.
Ning Li Yuanyuan Li Chengchao Zheng Jinguang Huang Shizhong Zhang 《Genes & genomics.》2016,38(8):723-731
Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons. 相似文献
8.
Rajkumari Sanjukta Mohammad Samir Farooqi Naveen Sharma Anil Rai Dwijesh Chandra Mishra Dhananjaya P Singh 《Bioinformation》2012,8(22):1087-1095
Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for
growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon
usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are
predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes
are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the
synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage
(RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural
selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the
codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly
and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and
may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory
functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study
could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to
develop salt-tolerant crops of agronomic value. 相似文献
9.
昆虫质型多角体病毒(cypovirus,CPV)是害虫种群重要调节因子,可用作生物防治剂。本研究采用多元统计分析方法对7种CPV进行密码子使用模式分析,结果表明:CPV密码子使用偏好性较弱,多数基因密码子使用模式受碱基组成影响,少数基因密码子使用模式除碱基组成外还有其它影响因素;中性绘图分析表明碱基组成主要受选择压力影响,受突变影响较小。同一电泳型CPV之间比同一宿主CPV之间共有的偏好性密码子多。CPV基因组内10个基因组片段之间密码子偏好性存在差异。CPV密码子偏好性与宿主昆虫密码子偏好性存在差异,所有CPV与其宿主昆虫共有的偏好性密码子均较少。对应分析进一步证明碱基组成是影响密码子使用的主要因素,不同电泳型CPV具有不同的密码子使用模式。聚类分析表明同一电泳型CPV密码子使用模式相似,同一宿主CPV密码子使用模式差异较大。 相似文献
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11.
Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level. 相似文献
12.
《Genomics》2020,112(1):304-311
Genetic changes in Hypoxanthine guanine phosphoribosyltransferace (HPRT1) gene can alter the expression of the dopamine neurotransmitter leads to abnormal neuron function, a disease called Lesch-Nyhan syndrome (LNS). Although different studies were conducted on LNS, information on codon usage bias (CUB) of HPRT1 gene is limited. The present study examines the genetic determinants of CUB in HPRT1 gene using twelve mammalian species. In the coding sequence of HPRT1 genes, A/T ending codons was most frequently used. A higher ENC value was observed indicating lower HPRT1 gene expression in the selected mammalian species. Correlation analysis indicates that compositional constraints under mutation pressure can involve in CUB of HPRT1 genes among the selected mammalian species. Relative synonymous codon usage (RSCU) value revealed that the codons such as ACT, AGG, ATT and AGC were over-represented in each of the mammalian species. Result from the analysis of the RSCU indicates that compositional constraint is a key driver for the variation in codon usage. Ratio of nonsynonymous (dN) and synonymous (dS) substitution further suggested that purifying selection occurs among the HPRT1 gene of studied mammals to maintain its protein function under the process of evolution. Our findings report an insight into the codon usage patterns of HPRT1 gene and will be useful for LNS management. 相似文献
13.
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.14.
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16.
Analysis of synonymous codon usage patterns in different plant mitochondrial genomes 总被引:1,自引:0,他引:1
Codon usage in mitochondrial genome of the six different plants was analyzed to find general patterns of codon usage in plant
mitochondrial genomes. The neutrality analysis indicated that the codon usage patterns of mitochondrial genes were more conserved
in GC content and no correlation between GC12 and GC3. T and A ending codons were detected as the preferred codons in plant
mitochondrial genomes. The Parity Rule 2 plot analysis showed that T was used more frequently than A. The ENC-plot showed that although a majority of the points with low ENC values were lying below the expected curve, a few genes lied on the expected curve. Correspondence analysis of relative synonymous
codon usage yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggest
that natural selection is likely to be playing a large role in codon usage bias in plant mitochondrial genomes, but not only
natural selection but also other several factors are likely to be involved in determining the selective constraints on codon
bias in plant mitochondrial genomes. Meantime, 1 codon (P. patens), 6 codons (Z. mays), 9 codons (T. aestivum), 15 codons (A. thaliana), 15 codons (M. polymorpha) and 15 codons (N. tabacum) were defined as the preferred codons of the six plant mitochondrial genomes. 相似文献
17.
Molecular Biology makes it possible to express foreign genes in microorganism, plants and animals. To improve the heterologous expression, it is important that the codon usage of sequence be optimized to make it adaptive to host organism. In this paper, a novel method based on Quantum-behaved Particle Swarm Optimization (QPSO) algorithm is developed to optimize the codon usage of synthetic gene. Compared to the existing probability methods, QPSO is able to generate better results when DNA/RNA sequence length is less than 6 Kb which is the commonly used range. While the software or web service based on probability method may not exclude all defined restriction sites when there are many undesired sites in the sequence, our proposed method can remove the undesired site efficiently during the optimization process. 相似文献
18.
Alan M. Johnson 《Journal of molecular evolution》1990,30(4):383-387
Summary The weight-averaged observed/expected dinucleotide frequencies for the sum total of the coding regions of fiveToxoplasma genes were compared with the same parameters previously determined for the coding regions of 21Plasmodium genes. In addition, codon usage in the fiveToxoplasma genes was compared with that in the 21Plasmodium genes, and the percent distribution of amino acids in theToxoplasma protein pool and thePlasmodium protein pool were compared with that in a general protein pool of 314 proteins. The results are consistent with the hypothesis that, contrary to currently held opinion, the generaToxoplasma andPlasmodium are not especially closely related. 相似文献
19.
The "expression measure" of a gene, E(g), is a statistic devised to predict the level of gene expression from codon usage bias. E(g) has been used extensively to analyze prokaryotic genome sequences. We discuss 2 problems with this approach. First, the formulation of E(g) is such that genes with the strongest selected codon usage bias are not likely to have the highest predicted expression levels; indeed the correlation between E(g) and expression level is weak among moderate to highly expressed genes. Second, in some species, highly expressed genes do not have unusual codon usage, and so codon usage cannot be used to predict expression levels. We outline a simple approach, first to check whether a genome shows evidence of selected codon usage bias and then to assess the strength of bias in genes as a guide to their likely expression level; we illustrate this with an analysis of Shewanella oneidensis. 相似文献
20.
密码子使用偏性(CUB)是生物体重要的进化特征,对研究物种进化、基因功能以及外源基因表达等具有重要科学意义。本研究利用糜子(Panicum miliaceum L.)叶绿体基因组中筛选出的53条蛋白编码序列,对其密码子使用模式及偏性进行了分析。结果表明,糜子叶绿体基因的有效密码子数(ENC)在37.14~61之间,多数密码子的偏性较弱。相对同义密码子使用度(RSCU)分析发现,RSCU > 1的密码子有32个,其中28个以A、U结尾,表明第3位密码子偏好使用A和U碱基。中性分析发现,GC3与GC12的相关性不显著,回归曲线斜率为0.2129,表明密码子偏性主要受到自然选择的影响;而ENC-plot分析发现大部分基因落在曲线的上方及周围,表明突变也影响了密码子偏性的形成。进一步的对应性分析发现,第1轴为主要影响因素,解释了17.92%的差异,其与ENC、GC3S值的相关性均达到显著水平,但与CBI、GCall不相关。最后,9个密码子被鉴定为糜子叶绿体基因组的最优密码子,糜子叶绿体基因组的密码子使用偏性可能受选择和突变共同作用。 相似文献