Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

• Published in: Viruses Vol. 14; no. 10; p. 2267
• Main Authors: Qin, Lang, Ding, Shiwen, Wang, Zhilei, Jiang, Runzhou, He, Zhen
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.10.2022; MDPI
• Subjects: Amino acids; Bias; Brassica oleracea; Codon; codon usage; composition bias; Diseases and pests; Food crops; Genes; Genetic aspects; Genetic diversity; Genomes; host adaptation; Host plants; Host-virus relationships; Mutation; Natural selection; Phylogenetics; Plant viruses; Population genetics; Population structure; Potyviridae; Proteins; RNA viruses; Statistical analysis; turnip mosaic virus; Use statistics; Virus diseases of plants; Virus research; Viruses; China; Greece; South Korea; Turkey; United Kingdom > UK; Iran; Belgium; Poland; Brazil; Italy; Germany; Russia
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v14102267

Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.