Departments of Pediatrics, Microbiology & Immunology, Epidemiology & Population Health, Obstetrics, Gynecology and Woman's Health, and Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA.
Viruses. 2023 Jul 26;15(8):1631. doi: 10.3390/v15081631.
Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.
普遍的净化选择作用于非同义替换，是乳头瘤病毒基因组历史的一个显著特征，但选择作用对 HPV 多样化的非编码 DNA 基序的影响及其漂变仍知之甚少。在这项研究中，我们对一千多个完整的基因组进行了系统发育分析，代表了 型、谱系和 SNP 变体，并使用主成分分析、祖先状态重建和系统发育独立对比来研究非编码 DNA 序列基序的数量和位置。对于古老分化的 型，四种核苷酸（A、C、G、T）的组成、密码子使用、三联体使用以及 13 个已建立的非编码 DNA 序列基序揭示了与遗传漂变一致的系统发育聚类。祖先状态重建和系统发育独立对比揭示了古老的基因组改变，特别是 CpG 和 APOBEC3 基序。我们进行的每种进化分析方法都支持一个意外的结论，即遗传漂变和不同的进化驱动力以不同的方式在连续的时期构建了 基因组，甚至延伸到最近形成的变异谱系中的差异。
