Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp.
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RESEARCH
Open Access
Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. Mikyung Je1,2, Hayeon Kim3 and Hyeon S. Son1,2*
Abstract Background: 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. Methods: 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. Results: 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. Conclusions: 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. Keywords: Mycovirus, Polymycovirus, AfuPmV-1, Codon usage pattern, RSCU
Background Mycoviruses are viruses that infect fungi and are known to be infectious to most fungal species. 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 [1, 2]. To date, research on mycoviruses has mainly focused on plant pathogenic fungi. The hypovirulence * Correspondence: [email protected] 1 SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea 2 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 Full list of author information is available at the end of the article
effect of mycoviruses in fungi has led to the development of biological control agents to reduc
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