Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus.

Area of Science:

• Plant virology
• Molecular evolution
• Genomics

Background:

• Turnip mosaic virus (TuMV) is a significant pathogen causing mosaic diseases in global vegetable crops.
• Previous research focused on TuMV's genetic variation, population structure, timescale, and migration.
• The codon usage patterns and host adaptation of TuMV remain underexplored.

Purpose of the Study:

• To investigate the codon usage bias and host adaptation of Turnip mosaic virus (TuMV).
• To analyze the compositional bias and codon usage patterns in TuMV protein-coding sequences.
• To identify the primary factors influencing TuMV codon usage and its preferred host.

Main Methods:

• Analysis of 184 non-recombinant TuMV sequences.
• Assessment of genomic compositional bias and codon usage.
• Statistical analysis of codon usage patterns, including natural selection and mutation pressure.
• Calculation of Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI).
• Similarity Index (SiD) analysis to determine host preference.

Main Results:

• TuMV displays relatively stable genomic composition with slightly lower codon usage in protein-coding sequences.
• Natural selection is identified as the primary factor influencing TuMV codon usage patterns, alongside mutation pressure.
• Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) indicate strong adaptation of TuMV genes to Brassica oleracea.
• Similarity Index (SiD) analysis supports Brassica oleracea as a potentially preferred host for TuMV.

Conclusions:

• This study offers the first comprehensive assessment of codon usage bias in Turnip mosaic virus (TuMV) based on complete genomes.
• Findings highlight the significant role of natural selection in shaping TuMV's codon usage.
• The results strongly suggest Brassica oleracea as a preferred host, providing crucial insights for future research on TuMV evolution and origins.