Synonymous Codon Usage Analysis of Three Narcissus Potyviruses.

Area of Science:

• Plant Virology
• Molecular Evolution
• Bioinformatics

Background:

• Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV), and narcissus yellow stripe virus (NYSV) are Potyviruses causing significant narcissus crop losses.
• Previous research focused on genetic diversity and evolution rates, but synonymous codon usage in these viruses remained unclear.

Purpose of the Study:

• To analyze the phylogenetic relationships and codon usage patterns of NDV, NLSYV, and NYSV using their coat protein (CP) genes.
• To investigate the factors influencing codon usage bias in these narcissus viruses.

Main Methods:

• Phylogenetic analysis of CP gene sequences from NDV, NLSYV, and NYSV isolates.
• Analysis of codon usage patterns, including Effective Number of Codons (ENC) and neutrality plots.
• Identification of optimal codons and preferred codon usage trends.

Main Results:

• Phylogenetic analysis revealed distinct clustering of isolates, often correlating with geographic distribution.
• Weak codon usage bias was observed in the CP coding regions of all three viruses.
• Natural selection was identified as the primary driver of codon usage bias, outweighing mutation pressure.
• A shared optimal codon (CCA) was found, with a preference for A/U-ending codons over C/G-ending ones.

Conclusions:

• This study provides the first codon usage analysis of multiple viruses infecting the same host (narcissus).
• Codon usage patterns are shaped by natural selection, indicating evolutionary adaptation.
• Understanding these evolutionary dynamics is crucial for developing effective, evolution-based strategies to control these economically important narcissus viruses.