Codon Usage Bias Analysis of Citrus Leaf Blotch Virus

Area of Science:

• Virology
• Genomics
• Evolutionary Biology

Background:

• Citrus leaf blotch virus (CLBV), a member of the Citrivirus genus, infects vital fruit crops like citrus, kiwifruit, and apples.
• High incidence rates in field surveys highlight CLBV as an emerging threat to global fruit production.
• Understanding CLBV genetic diversity is crucial for predicting epidemics and developing effective control strategies.

Purpose of the Study:

• To conduct the first genome-wide analysis of codon usage bias in Citrus leaf blotch virus (CLBV).
• To investigate the evolutionary forces shaping CLBV genetic diversity.
• To determine the influence of host adaptation on CLBV evolution.

Main Methods:

• Analysis of codon usage bias using all available CLBV full-length genomes.
• Phylogenetic analysis to categorize CLBV isolates.
• Evaluation of host influence on codon usage bias using the codon adaptation index.

Main Results:

• CLBV exhibits low codon usage bias, primarily driven by natural selection over mutational drift.
• Phylogenetic analysis revealed isolates cluster by host of origin, not geographical location, indicating host adaptation's importance.
• Cherry (Prunus avium) was identified as the host with the most significant influence on CLBV codon usage bias.

Conclusions:

• Host adaptation plays a more significant role than spatial structure in CLBV evolution.
• Natural selection is the dominant force shaping CLBV's codon usage landscape.
• This study provides a foundational genome-wide perspective on CLBV codon usage bias for future evolutionary research.