Comprehensive Analysis of Codon Usage on Porcine Astrovirus
| Autor: | Chunxiao Mou, Huiguang Wu, Jingwen Zhao, Zhengyu Bao, Zhenhai Chen |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Codon Adaptation Index Swine 030106 microbiology lcsh:QR1-502 porcine astrovirus (PAstV) Genome Viral Genome lcsh:Microbiology Article Astrovirus 03 medical and health sciences host adaptability Virology Astroviridae Infections Animals Codon Codon Usage Phylogeny codon usage pattern Genetics Swine Diseases mutation pressure Natural selection Phylogenetic tree biology phylogenetic analysis natural selection biology.organism_classification Adaptation Physiological 030104 developmental biology Infectious Diseases Porcine astrovirus Codon usage bias Mutation (genetic algorithm) Astroviridae |
| Zdroj: | Viruses Volume 12 Issue 9 Viruses, Vol 12, Iss 991, p 991 (2020) |
| ISSN: | 1999-4915 |
| DOI: | 10.3390/v12090991 |
| Popis: | Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns. |
| Databáze: | OpenAIRE |
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