Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp.
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...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | Virology Journal |
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| Online Access: | http://link.springer.com/article/10.1186/s12985-019-1115-y |
| _version_ | 1818543234015559680 |
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| author | Mikyung Je Hayeon Kim Hyeon S. Son |
| author_facet | Mikyung Je Hayeon Kim Hyeon S. Son |
| author_sort | Mikyung Je |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T22:32:40Z |
| format | Article |
| id | doaj.art-1a276aa8e9034016839afc9b13bb74d9 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-11T22:32:40Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-1a276aa8e9034016839afc9b13bb74d92022-12-22T00:48:05ZengBMCVirology Journal1743-422X2019-01-0116111010.1186/s12985-019-1115-yAnalysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp.Mikyung Je0Hayeon Kim1Hyeon S. Son2SNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National UniversityDepartment of Biomedical Laboratory Science, Kyungdong UniversitySNU Bioinformatics Institute, Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National UniversityAbstract 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.http://link.springer.com/article/10.1186/s12985-019-1115-yMycovirusPolymycovirusAfuPmV-1Codon usage patternRSCU |
| spellingShingle | Mikyung Je Hayeon Kim Hyeon S. Son Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. Virology Journal Mycovirus Polymycovirus AfuPmV-1 Codon usage pattern RSCU |
| title | Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. |
| title_full | Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. |
| title_fullStr | Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. |
| title_full_unstemmed | Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. |
| title_short | Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp. |
| title_sort | analysis of the codon usage pattern of the rdrp gene of mycovirus infecting aspergillus spp |
| topic | Mycovirus Polymycovirus AfuPmV-1 Codon usage pattern RSCU |
| url | http://link.springer.com/article/10.1186/s12985-019-1115-y |
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