为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:...为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:密码子第三位GC含量为27.55%,ENC范围在35.23~56.67之间,平均值为46.09;RSCU值大于1.00的密码子数目为30个,其中29个第三位碱基以U或A结尾;中性绘图表明GC12与GC3的相关系数为0.143,相关性不显著,回归系数为0.0573;频数分布显示,55%基因的ENC比值集中分布在0~0.1,25%基因的ENC比值分布在0.1~0.2之间;对应分析结果表明,第一向量轴占10.12%的差异,第二向量轴占9.36%的差异,其余两轴分别占7.97%和7.46%,前4轴累计差异为34.91%。中性绘图、ENC-plot和对应性分析均表明普通油茶叶绿体基因密码子偏好受突变作用,更多受选择的影响。最终取高表达优越密码子和高频密码子共有的CUU、AUU、GUU、GUA、UAA、CAA、AAA、GAC、GAA、CCU、ACU、GCU、GCA、UGU、CGU、AGU、UUG、GGU等18个密码子作为最优密码子。该研究结果为利用叶绿体基因工程技术改良普通油茶重要经济性状奠定了基础。展开更多
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
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
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
文摘为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:密码子第三位GC含量为27.55%,ENC范围在35.23~56.67之间,平均值为46.09;RSCU值大于1.00的密码子数目为30个,其中29个第三位碱基以U或A结尾;中性绘图表明GC12与GC3的相关系数为0.143,相关性不显著,回归系数为0.0573;频数分布显示,55%基因的ENC比值集中分布在0~0.1,25%基因的ENC比值分布在0.1~0.2之间;对应分析结果表明,第一向量轴占10.12%的差异,第二向量轴占9.36%的差异,其余两轴分别占7.97%和7.46%,前4轴累计差异为34.91%。中性绘图、ENC-plot和对应性分析均表明普通油茶叶绿体基因密码子偏好受突变作用,更多受选择的影响。最终取高表达优越密码子和高频密码子共有的CUU、AUU、GUU、GUA、UAA、CAA、AAA、GAC、GAA、CCU、ACU、GCU、GCA、UGU、CGU、AGU、UUG、GGU等18个密码子作为最优密码子。该研究结果为利用叶绿体基因工程技术改良普通油茶重要经济性状奠定了基础。
基金supported by the National Natural Science Foundation of China (31401822)
文摘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.
基金The work is supported by National Natural Science Foundation of China (No. 60121101).
文摘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.
文摘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.
