Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias

Ge Zhiyi; Li Xuerui; Cao Xiaoan; Wang Rui; Hu Wen; Gen Ling; Han Shengyi; Shang Youjun; Liu Yongsheng; Zhou Jian-hua

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Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias

机译：葡萄球菌噬菌体的病毒适应性：基于基于密码子使用偏差的选择性偏好的基于基于基于基于基于基于基于基于基于密码子的分析

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摘要

Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.

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《Genomics》 |2020年第6期|共9页
作者
Ge Zhiyi; Li Xuerui; Cao Xiaoan; Wang Rui; Hu Wen; Gen Ling; Han Shengyi; Shang Youjun; Liu Yongsheng; Zhou Jian-hua;
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作者单位

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Univ Southern Calif Viterbi Sch Engn Los Angeles CA 90089 USA;

Gansu Police Vocat Coll Lanzhou 730046 Gansu Peoples R China;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

Chinese Acad Agr Sci Lanzhou Vet Res Inst State Key Lab Vet Etiol Biol Lanzhou 730046 Gansu;

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原文格式 PDF
正文语种 eng
中图分类医学遗传学;
关键词
Staphylococcal phage; Synonymous codon usage; Host limitation; Phagic phenotype; Genome evolution;

机译：葡萄球菌噬菌体;同义密码子使用;宿主限制;噬菌体表型;基因组进化;

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专利

1. Factors Influencing the Synonymous Codon and Amino Acid Usage Bias in AT-rich Pseudomonas aeruginosa Phage PhiKZ [J] . K. SAU, S. SAU, S. C. MANDAL, 生物化学与生物物理学报：英文版 . 2005,第009期
2. Analysis of Synonymous Codon Usage Bias in 09H1N1 [J] . Zhen-peng LI, De-quan YING, Peng LI, 中国病毒学：英文版 . 2010,第005期
3. Analysis of Synonymous Codon Usage Bias in Chlamydia [J] . Hui L(ü), Wei-Ming ZHAO, Yan ZHENG, 生物化学与生物物理学报：英文版 . 2005,第001期
4. Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias [J] . Zhiyi Ge, Xuerui Li, Xiaoan Cao, Genomics . 2020,第6期

机译：病症适应金葡萄球菌噬菌体：基于密码子使用偏差的选择性偏好的基于基于基于基于基于基于基于基于基于基于因子的分析
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机译：对Crenarchaea和Euryarchaea基因组中密码子使用偏倚的比较分析显示，同义密码子对编码高度表达的核糖体和RNA聚合酶蛋白的偏好不同。
6. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins [J] . Baruah Vishwa Jyoti, Satapathy Siddhartha Sankar, Powdel Bhesh Raj, Journal of genetics . 2016,第3期

机译：对Crenarchaea和Euryarchaea基因组中密码子使用偏倚的比较分析显示，同义密码子对编码高度表达的核糖体和RNA聚合酶蛋白的偏好不同。
7. Analysis of Mutation Bias in Shaping Codon Usage Bias and Its Association with Gene Expression Across Specie [C] . Zhixiu Lu, Michael A. Gilchrist, Scott Emrich International Conference on Bioinformatics and Computational Biology . 2020

机译：成型密码子使用偏差突变偏差及其与物种基因表达的关系
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机译：多核苷酸解压缩，病毒密码子使用和晶体缺陷的生物物理学。
9. Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences [O] . Iris Bahir, Menachem Fromer, Yosef Prat, 2009

机译：病毒对宿主的适应性：基于蛋白质组的密码子使用和氨基酸偏好分析
10. Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences [O] . Bahir, Iris, Fromer, Menachem, Prat, Yosef, 2009

机译：病毒对宿主的适应性：基于蛋白质组的密码子使用和氨基酸偏好分析
11. Analysis of Selectivity Bias in the AAPCC [R] . Dowd, B., Feldman, R., Moscovice, I., 1993

机译：aapCC中选择性偏差的分析

Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias

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