SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
Laboratory of Computational Biology & Bioinformatics, Institute of Public Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
Virol J. 2019 Jan 16;16(1):10. doi: 10.1186/s12985-019-1115-y.
Mycoviruses that infect fungi generally do not have a significant effect on the host and, instead, reduce the toxicity of the fungi. However, recent studies have shown that polymycovirus-1, a mycovirus that infects Aspergillus species known to cause disease in humans, is related to increased virulence of the fungus.
Comparative analysis was performed of RdRP gene codon usage patterns of Aspergillus fumigatus polymycovirus-1 (AfuPmV-1) and other mycoviruses known to infect Aspergillus spp. to examine the genetic characteristics of AfuPmV-1. In addition, codon usage analysis was performed to determine whether the nucleotide composition and codon usage characteristics of AfuPmV-1 were also present in other polymycoviruses and hypervirulence-related mycoviruses. Phylogenetic analysis was also performed to investigate their evolutionary relationship.
Analysis of nucleotide composition indicated that AfuPmV-1 had the highest GC content among analyzed mycoviruses and relative synonymous codon usage analysis indicated that all of the codons preferred by AfuPmV-1 ended with C or G, while codons ending with A or U were not observed. Moreover, the effective number of codons, the codon adaptation index, and correspondence analysis showed that AfuPmV-1 had greater codon preference compared with other mycoviruses and that AfuPmV-1 had relatively high adaptability to humans and fungi. These results were generally similar among polymycoviruses.
The codon usage pattern of AfuPmV-1 differs from other mycoviruses that infect Aspergillus spp. This difference may be related to the hypervirulence effect of AfuPmV-1. Analysis of AfuPmV-1 codon usage patterns could contribute to the identification and prediction of virulence effects of mycoviruses with similar genetic characteristics.
感染真菌的真菌病毒通常对宿主没有显著影响，反而会降低真菌的毒性。然而，最近的研究表明，感染已知会引起人类疾病的曲霉菌属的多角体病毒-1（AfuPmV-1）与真菌毒力的增加有关。
对感染烟曲霉的多角体病毒-1（AfuPmV-1）和其他已知感染曲霉菌属的真菌病毒的 RdRP 基因密码子使用模式进行比较分析，以研究 AfuPmV-1 的遗传特征。此外，还进行了密码子使用分析，以确定 AfuPmV-1 的核苷酸组成和密码子使用特征是否也存在于其他多角体病毒和与高毒力相关的真菌病毒中。还进行了系统发育分析，以研究它们的进化关系。
核苷酸组成分析表明，AfuPmV-1 在分析的真菌病毒中具有最高的 GC 含量，相对同义密码子使用分析表明，AfuPmV-1 偏好的所有密码子都以 C 或 G 结尾，而没有观察到以 A 或 U 结尾的密码子。此外，有效密码子数、密码子适应指数和对应分析表明，AfuPmV-1 与其他真菌病毒相比具有更强的密码子偏好性，并且 AfuPmV-1 对人类和真菌具有相对较高的适应性。这些结果在多角体病毒中普遍相似。
AfuPmV-1 的密码子使用模式与感染曲霉菌属的其他真菌病毒不同。这种差异可能与 AfuPmV-1 的高毒力效应有关。分析 AfuPmV-1 的密码子使用模式有助于识别和预测具有相似遗传特征的真菌病毒的毒力效应。
