Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.

Xiaochun Tan, Siwen Bao, Xiaolei Lu, Binbin Lu, Weifeng Shen, Chaoyue Jiang
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Abstract

Human papillomavirus type 51 (HPV-51) is associated with various cancers, including cervical cancer. Examining the codon usage bias of the organism can offer valuable insights into its evolutionary patterns and its relationship with the host. This study comprehensively analyzed codon usage bias in HPV-51 by examining 64 complete genome sequences sourced from the NCBI GenBank database. Our analysis revealed no noteworthy preference for codon usage in HPV-51 overall. However, there was a noticeable bias towards A/T-ending codons, accompanied by GC3s below 32%. Dinucleotide frequency analysis revealed reduced frequencies for ApA, CpG, and TpC dinucleotides, while CpA and TpG dinucleotides were more frequent than others. Relative Synonymous Codon Usage analysis revealed 30 favored codons, primarily concluding with A/T nucleotides. Further analysis using Parity Rule 2, Effective Number of Codons plot, and neutrality plot indicated a balance between mutational pressure and natural selection, with natural selection being the primary force shaping codon usage bias. The Isoacceptor tRNA Pool analysis indicates that HPV-51 has a higher translation efficiency within the human cellular translational system. Moreover, the Codon Adaptation Index and Relative Codon Deoptimization Index analyses suggested a moderate adaptation of HPV-51 to human codon preferences. Our discoveries offer valuable perspectives on how HPV-51 evolves and uses genetic codes, contributing to a deeper comprehension of its endurance and disease-causing potential.

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全面分析人类乳头瘤病毒 51 型的密码子使用偏差。
人乳头瘤病毒 51 型(HPV-51)与包括宫颈癌在内的多种癌症有关。研究该生物体的密码子使用偏倚可以为了解其进化模式及其与宿主的关系提供有价值的信息。本研究通过研究来自 NCBI GenBank 数据库的 64 个完整基因组序列,全面分析了 HPV-51 的密码子使用偏向。我们的分析表明,HPV-51 的密码子使用总体上没有明显的偏好。但是,A/T 结尾的密码子有明显的偏向,同时 GC3 低于 32%。二核苷酸频率分析表明,ApA、CpG 和 TpC 二核苷酸的频率降低,而 CpA 和 TpG 二核苷酸的频率高于其他二核苷酸。相对同义密码子使用分析显示,有 30 个密码子受到青睐,主要以 A/T 核苷酸结尾。利用奇偶性规则 2、有效密码子数量图和中性图进行的进一步分析表明,突变压力和自然选择之间存在平衡,自然选择是形成密码子使用偏向的主要力量。等位 tRNA 库分析表明,HPV-51 在人体细胞翻译系统中具有更高的翻译效率。此外,密码子适应指数和相对密码子去优化指数分析表明,HPV-51 对人类密码子偏好的适应程度适中。我们的发现为了解 HPV-51 如何进化和使用遗传密码提供了宝贵的视角,有助于更深入地了解其耐力和致病潜力。
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