{"title":"探索拉拉病毒 DNA 聚合酶基因中的密码子使用模式和影响因素。","authors":"Yeşim Aktürk Dizman","doi":"10.1002/jobm.202400289","DOIUrl":null,"url":null,"abstract":"<div>\n \n <p>Ranaviruses, members of the genus <i>Ranavirus</i> within the family <i>Iridoviridae</i>, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from <i>Ranavirus</i>, <i>Lymphocystivirus</i>, <i>Megalocytivirus</i>, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of <i>Ranavirus</i>. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in <i>Ranavirus</i> DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of <i>Ranavirus</i> DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that <i>Ranavirus</i> DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of <i>Ranavirus</i> to its hosts.</p>\n </div>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes\",\"authors\":\"Yeşim Aktürk Dizman\",\"doi\":\"10.1002/jobm.202400289\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div>\\n \\n <p>Ranaviruses, members of the genus <i>Ranavirus</i> within the family <i>Iridoviridae</i>, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from <i>Ranavirus</i>, <i>Lymphocystivirus</i>, <i>Megalocytivirus</i>, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of <i>Ranavirus</i>. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in <i>Ranavirus</i> DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of <i>Ranavirus</i> DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that <i>Ranavirus</i> DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of <i>Ranavirus</i> to its hosts.</p>\\n </div>\",\"PeriodicalId\":15101,\"journal\":{\"name\":\"Journal of Basic Microbiology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-08-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Basic Microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/jobm.202400289\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Basic Microbiology","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/jobm.202400289","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
狂犬病毒是虹彩病毒科狂犬病毒属的成员,由于其对全球两栖动物和其他冷血脊椎动物构成了严重威胁,因此已成为两栖动物种群关注的焦点。我们利用生物信息学工具研究了来自拉纳病毒、淋巴囊病毒、巨细胞病毒和两种未分类的拉纳病毒的61个DNA pol基因的密码子使用模式,因为以前没有进行过这方面的研究。研究结果表明,在拉纳病毒的 DNA pol 基因中存在轻微或较低程度的密码子使用偏差(CUB)。核苷酸含量、第三密码子位置、有效密码子数(ENC)、对应分析(COA)、Aroma值和GRAVY值的相关分析表明,DNA pol基因的CUB可能受到突变压力和自然选择的影响。中性图表明,自然选择是驱动密码子使用的主要因素。此外,对密码子适应指数(CAI)的分析表明,拉尼亚病毒 DNA pol 基因对宿主具有很强的适应性。对相对密码子去优化指数(RCDI)的分析表明,拉尼亚病毒 DNA pol 基因承受了来自宿主的更大选择压力。这些发现将有助于理解影响拉尼亚病毒进化和适应宿主的因素。
Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes
Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.
期刊介绍:
The Journal of Basic Microbiology (JBM) publishes primary research papers on both procaryotic and eucaryotic microorganisms, including bacteria, archaea, fungi, algae, protozoans, phages, viruses, viroids and prions.
Papers published deal with:
microbial interactions (pathogenic, mutualistic, environmental),
ecology,
physiology,
genetics and cell biology/development,
new methodologies, i.e., new imaging technologies (e.g. video-fluorescence microscopy, modern TEM applications)
novel molecular biology methods (e.g. PCR-based gene targeting or cassettes for cloning of GFP constructs).