Phylogenetic analysis and genetic variation of Tomato yellow leaf curl virus based on the V1 gene in Iraq

Tomato yellow leaf curl virus (TYLCV) is a supreme pathogen in tropical and subtropical areas. During 2014-2015, a total of 393 tomato samples showing Tomato yellow leaf curl disease (TYLCD) symptoms were collected from six different provinces of Iraq. In serological assays, 55 out of 393 samples (14%) reacted positively with TYLCV-specific antibodies .The presence of TYLCV was verified in 21 (out of 55 samples showing tomato yellow leaf curl disease) samples by PCR. Coat protein gene (V1) of 16 TYLCV isolates was amplified using specific primers and cloned. Nucleotide sequence of Iraqi TYLCV isolates V1 gene shared the highest nucleotide sequence identity of 94.1-99.6% in CP gene with Kuwait and Iraq isolates. In phylogenetic analysis based on V1 nucleotide sequences, Iraqi isolates were separated into two main groups and three subgroups, without correlation with geographical origin. Genetic diversity parameters based on V1 nucleotide sequences indicated a high genetic variability in Iraqi population of TYLCV. The proportion of non-synonymous to synonymous nucleotide diversity was <1.0, indicating that this gene is under negative selection. A low gene flow was observed between southern and centric Iraq subpopulations, demonstrating genetic differentiation among Iraqi subpopulations. This is the first study dealt with distribution and genetic variation of TYLCV in Iraq. Full length viral genome sequencing of TYLCV isolates of Iraq is necessary to defferentiate virus strain(s) in Iraq.