Analysis of codon usage bias in potato virus Y non-recombinant strains
| Autor: | Juan Cristina, Mercedes Peyrou, Eduardo de Mello Volotão, Mariela Martínez Gómez, Isabel Rodríguez Assandri |
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| Rok vydání: | 2019 |
| Předmět: |
Cancer Research
Potyvirus Genome Viral Biology Virus 03 medical and health sciences Open Reading Frames Virology Genotype Codon Usage Phylogeny 030304 developmental biology Plant Diseases Solanum tuberosum Genetics 0303 health sciences Base Composition 030306 microbiology Potyviridae Genetic Variation biology.organism_classification Open reading frame Infectious Diseases Potato virus Y Codon usage bias PEST analysis Databases Nucleic Acid |
| Zdroj: | Virus research. 286 |
| ISSN: | 1872-7492 |
| Popis: | Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as well as it biological and molecular complexities have aroused great attention, thus several studies have explore it genetic characteristics. However, little is known about PVY codon usage. To shed light on the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of PVY non-recombinant strains (PVYN-NA, PVYEu-N, PVYO, PVYO5, PVYC) based on 130 complete open reading frame sequences extracted from public databases. Furthermore, similarities between the synonymous codon usage of PVY and its main hosts were investigated. The results obtained in the current study suggest that the overall codon usage among PVY genotypes is similar and slightly biased. PVY codon usage is strongly influenced by mutational bias, but also by G + C compositional constraint and dinucleotide composition. Furthermore, similarities among codon usage preferences between PVY strains and analyzed hosts were observed. |
| Databáze: | OpenAIRE |
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