National Center of Excellence in Molecular Biology (CEMB)
Abstract
Background: Keeping in view the potential damage caused by viruses to production of different crops and possible ‘directed damages’ by manipulated viral attack in/across border collectively make phylogenetic analysis of any attacking viral specie important. Cereal yellow dwarf viruses (CYDV) are highly important viruses in wheat causing significant yield loss.Methods: Double antibody sandwich ELISA and reverse transcription polymerase chain reaction (RT-PCR) was used to detect and confirm the polerovirus i.e. CYDV-rhopalosiphum padi virus (RPV), and unassigned viruses (SGV, RMV) in Punjab and NWFP provinces. The PCR products were inserted into a pGEM®-T easy vector, which then transformed in JM-107 cells of Escherichia coli. Recombinant plasmids were sequenced. Nucleotide and predicted amino acid sequences were aligned, analyzed and compared with other RPV isolates of the family. The nucleotide sequence data were used to make a phylogenetic tree.Results: Sequencing of 600 bp of coat protein gene confirmed the presence of CYDV-RPV strain. Pakistani isolate has close phylogenetic relationship with RPV-Mexcio and RPV-Yolo (USA). They had 99.95% similarity with RPV-Pakistan. The RPV-Aus, RPV-IR, and RPV-Cal (USA) had 99.94% identities with RPV-Pakistan.Conclusion: This work led to a conclusion that there is very low genetic diversity in RPV-Pakistan. Now it is in our future interest to clarify the identity of RPV-PK with more sequencing. The current study may help scientists to formulate appropriate management strategies against CYDV-RPV
