Evolutionary Analysis of Tomato Brown Rugose Fruit Virus Reveals Purifying Selection on the Coat Protein Gene

Document Type : Research Article

Authors

Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan, Iran

Abstract

Tomato (Solanum lycopersicum) is one of the world’s most economically important vegetable crops, yet its productivity is increasingly threatened by viral pathogens that reduce yield and fruit quality. Among emerging viruses, tomato brown rugose fruit virus (ToBRFV), a member of the genus Tobamovirus, has become a global concern due to its rapid mechanical and seed transmission and its capacity to infect both greenhouse and open-field tomato production systems. This study aimed to characterize the genetic diversity and evolutionary dynamics of ToBRFV populations in Iran using complete coat protein (CP) gene sequences. Twenty-eight symptomatic tomato samples were collected from greenhouses in located in Bam and Qanad , Kerman Province, of which five were confirmed as ToBRFV-positive via PCR targeting a 620 bp fragment of the CP gene. Phylogenetic analysis was performed using the Maximum Likelihood method in MEGA (Version 12.1), whereas population genetic parameters and neutrality tests (Tajima’s D; Fu and Li’s D and F) were estimated using DnaSP. Recombination events were assessed using multiple algorithms implemented in RDP4 (Version 4.8). The Iranian isolates exhibited high haplotype diversity (Hd = 0.9) but low nucleotide diversity (π = 0.01375), indicating substantial haplotypic variation despite overall sequence conservation. A dN/dS ratio of 0.598 indicated that the CP gene is under purifying selection, and no statistically supported recombination events were detected. These findings demonstrate that ToBRFV populations in Iran maintain considerable genetic diversity at the haplotype level while preserving evolutionary stability in the CP gene, reflecting its functional constraints and importance in viral fitness.

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References

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Journal of Genetic Resources
Volume 12, Issue 1
2026
Pages 84-93

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