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Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms 被引量:2
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作者 江澎 孙啸 陆祖宏 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第3期275-284,共10页
In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfol... In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639). The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes. 展开更多
关键词 codon usage bias relative synonymous codon usage (RSCU) Aeropyrum pernix K1
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Synonymous codon usage in Methanosarcina mazei str.Goe1 and other Euryarchaeota microorganisms
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作者 吴昊男 笪遥 +2 位作者 魏镓伟 江澎 陆祖宏 《Journal of Southeast University(English Edition)》 EI CAS 2007年第2期289-293,共5页
A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms (Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160... A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms (Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160). Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms' codon usage pattems. 展开更多
关键词 codon usage bias relative synonymous codon usage (RSCU) methanosarcina mazei str. Goel
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Genome-wide analysis of the synonymous codon usage patterns in apple 被引量:12
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作者 LI Ning SUN Mei-hong +2 位作者 JIANG Ze-sheng SHU Huai-rui ZHANG Shi-zhong 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2016年第5期983-991,共9页
Apple(Malus×domestica) has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent oppo... Apple(Malus×domestica) has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS(Statistical Product and Service Solutions) programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple. 展开更多
关键词 APPLE the synonymous codon usage patterns codon bias RSCU
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Evolutionary selection on synonymous codons in RNA G-quadruplex structural region
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作者 Xu Yuming Qi Ting +1 位作者 Gu Wanjun Lu Zuhong 《Journal of Southeast University(English Edition)》 EI CAS 2021年第2期177-183,共7页
To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-c... To investigate how synonymous codons have been adapted to the formation of ribonucleic acid(RNA)G-quadruplex(rG4)structure,a computational searching algorithm G4Hunter was applied to detect rG4 structures in protein-coding sequences of mRNAs in five eukaryotic species.The native sequences forming rG4s were then compared with randomized sequences to evaluate selection on synonymous codons.Factors that may influence the formation of rG4 were also investigated,and the selection pressures of rG4 in different gene regions were compared to explore its potential roles in gene regulation.The results show universal selective pressure acts on synonymous codons in rG4 regions to facilitate rG4 formation in five eukaryotic organisms.While G-rich codon combinations are preferred in the rG4 structural region,C-rich codon combinations are selectively unfavorable for rG4 formation.Gene's codon usage bias,nucleotide composition,and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species.Moreover,rG4 structures in the translational initiation region showed significantly higher selective pressures than those in the translational elongation region. 展开更多
关键词 ribonucleic acid(RNA)structure G-QUADRUPLEX synonymous codons evolution SELECTION
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Genome-Wide Patterns of Codon Usage in the Pacific Oyster Genome
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作者 SONG Kai 《Journal of Ocean University of China》 SCIE CAS CSCD 2021年第5期1175-1182,共8页
The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same genome.Mutational processes or natural selective... The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same genome.Mutational processes or natural selective pressures affect this bias.However,a systematic investigation of codon usage pattern for molluscan species and its association with the two factors hasn’t been conducted.In this study,the whole genome codon usage patterns in oyster genome is investigated using the relative synonymous codon usage(RSCU)method,and 17 putative optimal codons were identified,wherein most had either a cytosine(C)or guanine(G)residue at the third position.Results showed that codon bias was positively associated with gene expression levels and breadth.Optimal codons had different mutational bias patterns compared with nonoptimal codons.Moreover,the results show that codon bias is negatively associated with nucleotide diversity.In the oyster genome,the fourfold degenerate codons are affected by different selective pressures,which can be regarded as an evidence that natural selection shapes codon usage patterns.This research will help to understand how natural selection and mutation bias affect codon usage in Mollusca genomes. 展开更多
关键词 codon bias synonymous codons gene expression nucleotide diversity Crassostrea gigas
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Comparative Multivariate Analysis of Codon and Amino Acid Usage in Three Leishmania Genomes
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作者 Nutan Chauhan Ambarish Sharan Vidyarthi Raju Poddar 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2011年第6期218-228,共11页
Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and tra... Multivariate analysis of codon and amino acid usage was performed for three Leishmania species, including L. donovani, L. infantum and L. major. It was revealed that all three species are under mutational bias and translational selection. Lower GC12 and higher GC3s in all three parasites suggests that the ancestral highly expressed genes (HEGs), compared to lowly expressed genes (LEGs), might have been rich in AT-content. This also suggests that there must have been a faster rate of evolution under GC-bias in LEGs. It was observed from the esti- mation of synonymous/non-synonymous substitutions in HEGs that the HEG dataset of L. donovani is much closer to L. major evolutionarily. This is also supported by the higher ds value as compared to ds between L. donovani and L. major, suggesting the conservation of synonymous codon positions between these two species and the role of translational selection in shaping the composition of protein-coding genes. 展开更多
关键词 LEISHMANIA relative synonymous codon usage multivariate analysis HYDROPATHY AROMATICITY
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