Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences

Area of Science:

• Plant virology
• Molecular evolution
• Bioinformatics

Background:

• Sugarcane mosaic virus (SCMV) causes significant mosaic diseases in graminaceous plants like maize and sugarcane.
• Previous studies focused on SCMV genetic variation and population structure, leaving evolutionary dynamics and codon usage patterns unclear.

Purpose of the Study:

• To investigate the evolutionary dynamics, synonymous codon usage, and adaptive evolution of Sugarcane mosaic virus (SCMV).
• To analyze phylodynamics and genomic composition bias of SCMV using complete genomic sequences.

Main Methods:

• Phylogenetic analysis of 108 complete SCMV genomic sequences.
• Analysis of genomic composition bias and codon usage patterns.
• Calculation of Codon Adaptation Index (CAI), Relative Codon Deoptimization Index (RCDI), and Similarity Index (SiD).

Main Results:

• Six host- and geographically confined phylogenetic lineages were identified within SCMV non-recombinant isolates.
• SCMV exhibits stable genomic composition with lower codon usage bias in protein-coding sequences.
• Natural selection is the dominant factor shaping SCMV codon usage, with a stronger correlation observed between SCMV and maize.

Conclusions:

• This study provides the first comprehensive evaluation of SCMV codon usage patterns based on complete sequences.
• Findings enhance understanding of SCMV's origin and evolutionary trajectory.
• Results suggest natural selection plays a key role in SCMV adaptation and host interaction.