Xudong Liu, Kexin Li, Xiaojing Chen, Yaqian Li, Tianshu Sun, Roujie Huang, Yanan Shi, Zilong He, Lei Li
{"title":"Codon Usage Pattern of Papillomavirus E6, E7, and L1 Genes Across Hosts.","authors":"Xudong Liu, Kexin Li, Xiaojing Chen, Yaqian Li, Tianshu Sun, Roujie Huang, Yanan Shi, Zilong He, Lei Li","doi":"10.1007/s00284-025-04468-8","DOIUrl":null,"url":null,"abstract":"<p><p>This study investigates the codon usage preferences of papillomaviruses across different hosts and examines the evolutionary relationships of key genes (L1, E6, and E7). Complete genome sequences of 86 papillomavirus strains were retrieved from the PaVE database. Phylogenetic trees were constructed using MAFFT and ITOL, and codon usage indices, including RSCU, ENC, CAI, and GC3, were calculated using CodonW. ENC-GC3, Neutrality, and PR2-bias analyses were conducted to explore the factors shaping codon usage patterns. The analyzed genomes were categorized into five groups (Clade1, Clade2, Clade3, Clade4, and Others), exhibiting variations in CAI and ENC values. Phylogenetic analysis revealed three distinct gene clusters. ENC-GC3, Neutrality, and PR2-bias analyses demonstrated that both natural selection and mutation pressure influence codon usage. These findings suggest that codon usage preferences and the evolutionary dynamics of L1, E6, and E7 genes differ across hosts, driven by a combination of selection and mutational forces.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":"82 10","pages":"481"},"PeriodicalIF":2.6000,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current Microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s00284-025-04468-8","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
This study investigates the codon usage preferences of papillomaviruses across different hosts and examines the evolutionary relationships of key genes (L1, E6, and E7). Complete genome sequences of 86 papillomavirus strains were retrieved from the PaVE database. Phylogenetic trees were constructed using MAFFT and ITOL, and codon usage indices, including RSCU, ENC, CAI, and GC3, were calculated using CodonW. ENC-GC3, Neutrality, and PR2-bias analyses were conducted to explore the factors shaping codon usage patterns. The analyzed genomes were categorized into five groups (Clade1, Clade2, Clade3, Clade4, and Others), exhibiting variations in CAI and ENC values. Phylogenetic analysis revealed three distinct gene clusters. ENC-GC3, Neutrality, and PR2-bias analyses demonstrated that both natural selection and mutation pressure influence codon usage. These findings suggest that codon usage preferences and the evolutionary dynamics of L1, E6, and E7 genes differ across hosts, driven by a combination of selection and mutational forces.
期刊介绍：
Current Microbiology is a well-established journal that publishes articles in all aspects of microbial cells and the interactions between the microorganisms, their hosts and the environment.
Current Microbiology publishes original research articles, short communications, reviews and letters to the editor, spanning the following areas:
physiology, biochemistry, genetics, genomics, biotechnology, ecology, evolution, morphology, taxonomy, diagnostic methods, medical and clinical microbiology and immunology as applied to microorganisms.
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