Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.
Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.
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DOI：
10.1371/journal.pone.0090905
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Tong Y
中科院分区：
文献类型：
--
作者：
Butt AM;Nasrullah I;Tong Y
基孔肯雅病毒（CHIKV）是披膜病毒科的节肢动物传播的病毒，其通过伊蚊属（Aedes spp.）蚊子其基因组由12 kb的单链正义RNA组成。在本研究中，我们报告的模式同义密码子的使用在141 CHIKV基因组中，通过计算几个密码子的使用指数和应用多元统计方法。相对同义密码子使用率（RSCU）分析表明，G/C和A-末端为首选同义密码子。CHIKV与其宿主的RSCU比较分析表明，CHIKV的密码子使用模式是一致和拮抗的混合。相似性指数分析表明，CHIKV的总体密码子使用模式在进化过程中受到黑猩猩和白纹伊蚊的强烈影响。从有效密码子数（ENC）和密码子适应指数（CAI）分析推断，CHIKV基因组中的总体密码子使用偏倚较低。我们的数据表明，尽管突变压力主导CHIKV中的密码子使用，但CHIKV中的密码子使用模式也受到来自其宿主和地理的自然选择的影响。据我们所知，这是第一个报告描述密码子使用分析在CHIKV基因组。这项研究的发现有望增加我们对病毒进化所涉及的因素以及对宿主和环境的适应性的理解。
Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
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DOI：
10.1016/j.meegid.2011.02.018
发表时间：
2011-07
期刊：
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
影响因子：
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作者：
Liu YS;Zhou JH;Chen HT;Ma LN;Pejsak Z;Ding YZ;Zhang J
通讯作者：
Zhang J
影响因子：
6.7
作者：
Greenbaum BD;Levine AJ;Bhanot G;Rabadan R
通讯作者：
Rabadan R
影响因子：
3.7
作者：
Lobo FP;Mota BE;Pena SD;Azevedo V;Macedo AM;Tauch A;Machado CR;Franco GR
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Franco GR