Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability

Area of Science:

• Plant virology
• Molecular evolution
• Genomics

Background:

• Cotton leafroll dwarf virus (CLRDV) emerged in the US in 2017 and has spread across southern cotton-growing regions.
• Understanding CLRDV genomic diversity is crucial for managing its impact on cotton production.

Purpose of the Study:

• To investigate the genomic variability and evolutionary patterns of CLRDV isolates in the United States.
• To compare US CLRDV isolates with those from South America.

Main Methods:

• Sequencing of eight complete CLRDV genomes from infected cotton plants in Alabama, Florida, and Texas.
• Phylogenetic analysis using Bayesian methods to determine evolutionary relationships.
• Analysis of nucleotide and amino acid sequence identity, recombination patterns, and selective pressures (dN/dS ratios).

Main Results:

• US CLRDV genomes (5865-5867 bp) showed high nucleotide identity (95.9-98.7%) among themselves.
• Open reading frame (ORF) 0, encoding the P0 protein, was the most variable gene.
• US isolates formed a distinct monophyletic group, separate from South American genotypes, indicating phylogeographical structuring.
• Recombination was prevalent, particularly in ORFs 2, 3, and 5.
• Purifying selection was identified as the main force shaping viral protein evolution (dN/dS < 1).

Conclusions:

• US CLRDV isolates exhibit significant genomic variability and distinct phylogeographical structuring compared to South American strains.
• The P0 protein's variability and recombination patterns are key features of CLRDV evolution in the US.
• Purifying selection plays a dominant role in CLRDV protein evolution, despite observed genetic diversity.