Molecular Identification, Analysis, and Sequencing of the Coat Protein Gene of Tomato yellow leaf curl virus in Tomato Fields from Selected Regions of Iran

Tomato yellow leaf curl virus (TYLCV; Begomovirus coheni) is one of the most destructive plant viruses worldwide, causing severe yield losses in tomato fields. In this study, field surveys were conducted in tomato-growing areas of Isfahan, Yazd, and Varamin (central Iran) to detect and investigate the genetic diversity of TYLCV. Leaf samples showing virus-like symptoms were collected, and total DNA was extracted for molecular detection. PCR amplification using V1 gene-specific primers resulted in a ~670 bp fragment in 12 suspected samples, of which seven isolates were selected for sequencing. The obtained sequences were aligned with reference sequences from GenBank, and phylogenetic analyses were performed using the Neighbor-Joining method in MEGA11. The results revealed that selected Iranian isolates clustered into two distinct groups within clade I, along with isolates from other parts of the world. Haplotype network analysis further supported these groupings. Notably, phylogenetic placement and strain-level classification of the newly identified isolates showed that all seven Iranian isolates (PV579121–PV579127) clustered within the TYLCV-OM group, forming a distinct lineage. This close genetic relationship suggests a common evolutionary origin and supports the hypothesis that these isolates belong to a region-specific strain adapted to the environmental conditions of central Iran. Genetic diversity analyses revealed significant differences among virus populations from the surveyed regions. Furthermore, neutrality tests (Tajima’s D, Fu and Li’s D* and F*) and population genetic analyses provided evidence of purifying selection and recent population expansion. One significant recombination event was also detected using RDP4 software. Selection pressure analysis using FEL and MEME methods identified several codons under both positive and negative selection. Collectively, these findings provide a comprehensive picture of the genetic diversity and evolutionary dynamics of TYLCV in central Iran and offer valuable insights for developing effective regional disease management strategies.