Nucleotide composition analysis was conducted based on the overall frequency of nucleic acid occurrence (A%, C%, U%, and G%), total AU%/GC%, frequency of the third nucleic acid in synonymous codons (A3s, C3s, U3 s, and G3 s), and the GC3s values.
The programs CodonW ( ) and CALcal ( ) were used to conduct analyses of nucleotide composition, overall/local G + C content, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and correspondence analysis (COA) for each of the selected genetic data. AfuTmV-1 was renamed AfuPmV-1, and its virus family name was changed from Tetramycoviridae to Polymycoviridae as more viruses showing similar characteristics to AfuTmV-1 were discovered, including BbPmV-1, which infects the insect pathogenic fungus, Beauveria bassiana (Table 1). In 2015, the A78 virus, which infects the human pathogenic fungus, Aspergillus fumigatus, was reported to have significant mild hypervirulence effects in the moth species, Galleria mellonella, and similar virulence effects have been reported in Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1) found in the same fungus. There have been relatively few studies on the hypervirulence effect of mycoviruses, although some results have been reported recently. The hypovirulence effect of mycoviruses in fungi has led to the development of biological control agents to reduce the virulence of fungi on important crops and plant resources. To date, research on mycoviruses has mainly focused on plant pathogenic fungi. While mycoviruses have little or no influence on the fungal host in most cases, some have been shown to control the pathogenicity of the host by increasing or decreasing the virulence. Mycoviruses are viruses that infect fungi and are known to be infectious to most fungal species. Analysis of AfuPmV-1 codon usage patterns could contribute to the identification and prediction of virulence effects of mycoviruses with similar genetic characteristics. This difference may be related to the hypervirulence effect of AfuPmV-1. The codon usage pattern of AfuPmV-1 differs from other mycoviruses that infect Aspergillus spp. These results were generally similar among polymycoviruses. 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. ResultsĪnalysis 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. Phylogenetic analysis was also performed to investigate their evolutionary relationship. 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. to examine the genetic characteristics of AfuPmV-1. MethodsĬomparative analysis was performed of RdRP gene codon usage patterns of Aspergillus fumigatus polymycovirus-1 (AfuPmV-1) and other mycoviruses known to infect Aspergillus spp. 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. Mycoviruses that infect fungi generally do not have a significant effect on the host and, instead, reduce the toxicity of the fungi.
0 kommentar(er)
