• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

基孔肯雅病毒密码子使用情况及其影响因素的全基因组分析

Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.

作者信息

Butt Azeem Mehmood, Nasrullah Izza, Tong Yigang

机构信息

Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.

Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.

出版信息

PLoS One. 2014 Mar 4;9(3):e90905. doi: 10.1371/journal.pone.0090905. eCollection 2014.

DOI:10.1371/journal.pone.0090905
PMID:24595095
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3942501/
Abstract

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.

摘要

基孔肯雅病毒（CHIKV）是披膜病毒科的一种节肢动物传播病毒，通过伊蚊属蚊子传播给人类。其基因组由一个12 kb的单链正义RNA组成。在本研究中，我们通过计算几个密码子使用指数并应用多元统计方法，报告了141个基孔肯雅病毒基因组中的同义密码子使用模式。相对同义密码子使用（RSCU）分析表明，偏好的同义密码子以G/C结尾且A在第三位。基孔肯雅病毒与其宿主之间的RSCU比较分析表明，基孔肯雅病毒的密码子使用模式是巧合与拮抗的混合。相似性指数分析表明，在进化过程中，黑猩猩和白纹伊蚊对基孔肯雅病毒的整体密码子使用模式产生了强烈影响。从有效密码子数（ENC）和密码子适应指数（CAI）分析推断，基孔肯雅病毒基因组中的整体密码子使用偏好较低。我们的数据表明，虽然突变压力在基孔肯雅病毒的密码子使用中占主导地位，但基孔肯雅病毒的密码子使用模式也受到其宿主和地理环境自然选择的影响。据我们所知，这是第一篇描述基孔肯雅病毒基因组密码子使用分析的报告。本研究的结果有望增进我们对病毒进化、对宿主和环境适应性相关因素的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/479917207eec/pone.0090905.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/f1d01b74c0b2/pone.0090905.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/5bcffaf148be/pone.0090905.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/c0ecbb32bc43/pone.0090905.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/33fb1257dbe5/pone.0090905.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/0b4d6ecdfc59/pone.0090905.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/4b7dc8ff5016/pone.0090905.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/81813c1093ec/pone.0090905.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/479917207eec/pone.0090905.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/f1d01b74c0b2/pone.0090905.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/5bcffaf148be/pone.0090905.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/c0ecbb32bc43/pone.0090905.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/33fb1257dbe5/pone.0090905.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/0b4d6ecdfc59/pone.0090905.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/4b7dc8ff5016/pone.0090905.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/81813c1093ec/pone.0090905.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/95ac/3942501/479917207eec/pone.0090905.g008.jpg

相似文献

1
Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.基孔肯雅病毒密码子使用情况及其影响因素的全基因组分析
PLoS One. 2014 Mar 4;9(3):e90905. doi: 10.1371/journal.pone.0090905. eCollection 2014.
2
Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells.随机密码子重编码可稳定降低基孔肯雅病毒在灵长类动物和蚊子细胞中的复制适应性。
PLoS Pathog. 2013 Feb;9(2):e1003172. doi: 10.1371/journal.ppat.1003172. Epub 2013 Feb 21.
3
Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.马流感病毒全基因组密码子使用偏好性的影响因素揭示
PLoS One. 2016 Apr 27;11(4):e0154376. doi: 10.1371/journal.pone.0154376. eCollection 2016.
4
Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts.克里米亚-刚果出血热病毒密码子使用偏性分析及其对宿主的适应性。
Infect Genet Evol. 2018 Mar;58:1-16. doi: 10.1016/j.meegid.2017.11.027. Epub 2017 Dec 6.
5
Sequential adaptive mutations enhance efficient vector switching by Chikungunya virus and its epidemic emergence.连续适应性突变增强了基孔肯雅病毒的高效载体转换及其流行出现。
PLoS Pathog. 2011 Dec;7(12):e1002412. doi: 10.1371/journal.ppat.1002412. Epub 2011 Dec 8.
6
Chikungunya virus and the mosquito vector Aedes aegypti in New Caledonia (South Pacific Region).新喀里多尼亚（南太平洋地区）的基孔肯雅病毒和媒介伊蚊
Vector Borne Zoonotic Dis. 2012 Dec;12(12):1036-41. doi: 10.1089/vbz.2011.0937. Epub 2012 Nov 20.
7
Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution.密码子使用情况的基因组分析表明，突变压力、自然选择和宿主特征对马尔堡病毒的进化产生影响。
BMC Evol Biol. 2015 Aug 26;15:174. doi: 10.1186/s12862-015-0456-4.
8
Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts.寨卡病毒同义密码子使用偏好性分析及其对宿主的适应性
PLoS One. 2016 Nov 28;11(11):e0166260. doi: 10.1371/journal.pone.0166260. eCollection 2016.
9
Differential Transmission of Antiviral Drug-Resistant Chikungunya Viruses by Mosquitoes.蚊虫对具有抗药性的基孔肯雅病毒的差异传播。
mSphere. 2018 Aug 22;3(4):e00230-18. doi: 10.1128/mSphere.00230-18.
10
High level of vector competence of Aedes aegypti and Aedes albopictus from ten American countries as a crucial factor in the spread of Chikungunya virus.来自十个美洲国家的埃及伊蚊和白纹伊蚊具有较高的媒介效能，是基孔肯雅热病毒传播的关键因素。
J Virol. 2014 Jun;88(11):6294-306. doi: 10.1128/JVI.00370-14. Epub 2014 Mar 26.

引用本文的文献

1
Decoding codon usage in human papillomavirus type 59.解读人乳头瘤病毒59型的密码子使用情况。
Virus Genes. 2025 Jun;61(3):313-323. doi: 10.1007/s11262-025-02148-0. Epub 2025 Mar 4.
2
Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.解读高危型人乳头瘤病毒基因组中的密码子使用模式：一项综合分析
Curr Microbiol. 2025 Feb 22;82(4):148. doi: 10.1007/s00284-025-04131-2.
3
Comparative genetic analysis of pathogenic and attenuated strains of Junín virus.胡宁病毒致病株与减毒株的比较遗传分析

本文引用的文献

1
Synonymous codon usage in TTSuV2: analysis and comparison with TTSuV1.TTSuV2 中的同义密码子使用：与 TTSuV1 的分析与比较。
PLoS One. 2013 Nov 26;8(11):e81469. doi: 10.1371/journal.pone.0081469. eCollection 2013.
2
The distribution of synonymous codon choice in the translation initiation region of dengue virus.登革热病毒翻译起始区同义密码子选择的分布。
PLoS One. 2013 Oct 25;8(10):e77239. doi: 10.1371/journal.pone.0077239. eCollection 2013.
3
A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection.
Genetica. 2025 Feb 8;153(1):12. doi: 10.1007/s10709-025-00228-5.
4
Analysis of synonymous codon usage bias of Lassa virus.拉沙病毒同义密码子使用偏好性分析
Virus Res. 2025 Mar;353:199528. doi: 10.1016/j.virusres.2025.199528. Epub 2025 Jan 29.
5
SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.SARS-CoV-2 在人类细胞中表现出低效的翻译密码子使用偏性，这种偏性是通过劫持 tRNA 表观转录组实现的。
Int J Mol Sci. 2024 Oct 29;25(21):11614. doi: 10.3390/ijms252111614.
6
Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.人乳头瘤病毒51型密码子使用偏好性的综合分析
Pol J Microbiol. 2024 Oct 28;73(4):455-465. doi: 10.33073/pjm-2024-036. eCollection 2024 Dec 1.
7
Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution.密码子使用偏好性：影响囊泡谷氨酸转运体发育表达和蛋白质进化的潜在因素。
Mol Neurobiol. 2025 Mar;62(3):3508-3522. doi: 10.1007/s12035-024-04426-8. Epub 2024 Sep 21.
8
Dengue virus preferentially uses human and mosquito non-optimal codons.登革热病毒优先使用人类和蚊子非最佳密码子。
Mol Syst Biol. 2024 Oct;20(10):1085-1108. doi: 10.1038/s44320-024-00052-7. Epub 2024 Jul 22.
9
Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.新博病毒的综合基因组学研究揭示了不同的密码子使用模式和宿主特异性。
Microorganisms. 2024 Mar 29;12(4):696. doi: 10.3390/microorganisms12040696.
10
Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts.克里米亚-刚果出血热病毒适应不同蜱类宿主的遗传背景。
PLoS One. 2024 Apr 25;19(4):e0302224. doi: 10.1371/journal.pone.0302224. eCollection 2024.
DNA 和 RNA 病毒基因组中同义密码子使用偏好模式的比较：量化突变压力和自然选择的相对重要性。
Biomed Res Int. 2013;2013:406342. doi: 10.1155/2013/406342. Epub 2013 Oct 2.
4
CpG usage in RNA viruses: data and hypotheses.RNA 病毒中的 CpG 运用：数据与假说。
PLoS One. 2013 Sep 23;8(9):e74109. doi: 10.1371/journal.pone.0074109. eCollection 2013.
5
A detailed comparative analysis on the overall codon usage patterns in West Nile virus.对西尼罗河病毒整体密码子使用模式的详细比较分析。
Infect Genet Evol. 2013 Mar;14:396-400. doi: 10.1016/j.meegid.2013.01.001. Epub 2013 Jan 16.
6
Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1).分析扭结瘤病毒 1（TTSuV1）中的同义密码子使用模式。
Arch Virol. 2013 Jan;158(1):145-54. doi: 10.1007/s00705-012-1480-y. Epub 2012 Sep 26.
7
Selective pressure dominates the synonymous codon usage in parvoviridae.选择压力主导细小病毒科中的同义密码子使用。
Virus Genes. 2013 Feb;46(1):10-9. doi: 10.1007/s11262-012-0818-6. Epub 2012 Sep 21.
8
Sequential adaptive mutations enhance efficient vector switching by Chikungunya virus and its epidemic emergence.连续适应性突变增强了基孔肯雅病毒的高效载体转换及其流行出现。
PLoS Pathog. 2011 Dec;7(12):e1002412. doi: 10.1371/journal.ppat.1002412. Epub 2011 Dec 8.
9
The characteristic of codon usage pattern and its evolution of hepatitis C virus.丙型肝炎病毒密码子使用模式及其进化特征。
Infect Genet Evol. 2011 Dec;11(8):2098-102. doi: 10.1016/j.meegid.2011.08.025. Epub 2011 Sep 1.
10
The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern.肠道病毒 71 型病毒同义密码子使用特征及其在密码子使用模式上受宿主的影响。
Infect Genet Evol. 2011 Jul;11(5):1168-73. doi: 10.1016/j.meegid.2011.02.018. Epub 2011 Mar 5.